Back to Long Tests report for BioC 3.20 |
This page was generated on 2024-07-06 23:55 -0400 (Sat, 06 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4643 |
palomino6 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4414 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4442 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 6/32 | Hostname | OS / Arch | CHECK | |||||||
biodbChebi 1.11.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | |||||||
palomino6 | Windows Server 2022 Datacenter / x64 | OK | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | ||||||||
To the developers/maintainers of the biodbChebi package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: biodbChebi |
Version: 1.11.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbChebi_1.11.0.tar.gz |
StartedAt: 2024-07-06 16:01:02 -0400 (Sat, 06 Jul 2024) |
EndedAt: 2024-07-06 16:04:34 -0400 (Sat, 06 Jul 2024) |
EllapsedTime: 212.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: biodbChebi.Rcheck |
Warnings: 0 |
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > # Script needed to run testthat automatically from ‘R CMD check’. See > # testthat::test_dir documentation. > library(testthat) > library(biodbChebi) > Sys.setenv(TESTTHAT_REPORTER="summary") > Sys.setenv(BIODB_LOG_DST="console") > test_check("biodbChebi") biodb.INFO [2024-07-06 16:01:39.151][biodb::testContext] biodb.INFO [2024-07-06 16:01:39.153][biodb::testContext] ******************************************************************************** biodb.INFO [2024-07-06 16:01:39.154][biodb::testContext] Test context - Generic long tests biodb.INFO [2024-07-06 16:01:39.155][biodb::testContext] ******************************************************************************** biodb.INFO [2024-07-06 16:01:39.156][biodb::testContext] biodb.INFO [2024-07-06 16:01:39.163][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.13.0. biodb.DEBUG[2024-07-06 16:01:39.165][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml". biodb.DEBUG[2024-07-06 16:01:39.173][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-07-06 16:01:39.174][self$getConfig()$define] Define config key allow.huge.downloads. biodb.DEBUG[2024-07-06 16:01:39.175][self$set] Set key allow.huge.downloads to TRUE. biodb.DEBUG[2024-07-06 16:01:39.176][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.179][self$getConfig()$define] Define config key autoload.extra.pkgs. biodb.DEBUG[2024-07-06 16:01:39.199][self$set] Set key autoload.extra.pkgs to TRUE. biodb.DEBUG[2024-07-06 16:01:39.200][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.203][self$getConfig()$define] Define config key cache.all.requests. biodb.DEBUG[2024-07-06 16:01:39.204][self$set] Set key cache.all.requests to TRUE. biodb.DEBUG[2024-07-06 16:01:39.205][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.208][self$getConfig()$define] Define config key cache.directory. biodb.DEBUG[2024-07-06 16:01:39.209][self$getConfig()$define] Define config key cache.read.only. biodb.DEBUG[2024-07-06 16:01:39.210][self$set] Set key cache.read.only to FALSE. biodb.DEBUG[2024-07-06 16:01:39.211][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.213][self$getConfig()$define] Define config key cache.subfolders. biodb.DEBUG[2024-07-06 16:01:39.214][self$getConfig()$define] Define config key cache.system. biodb.DEBUG[2024-07-06 16:01:39.215][self$set] Set key cache.system to TRUE. biodb.DEBUG[2024-07-06 16:01:39.216][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.219][self$getConfig()$define] Define config key use.cache.for.local.db. biodb.DEBUG[2024-07-06 16:01:39.220][self$set] Set key use.cache.for.local.db to FALSE. biodb.DEBUG[2024-07-06 16:01:39.221][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.224][self$getConfig()$define] Define config key dwnld.chunk.size. biodb.DEBUG[2024-07-06 16:01:39.225][self$getConfig()$define] Define config key dwnld.timeout. biodb.DEBUG[2024-07-06 16:01:39.226][self$set] Set key dwnld.timeout to 3600. biodb.DEBUG[2024-07-06 16:01:39.227][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.230][self$getConfig()$define] Define config key compute.fields. biodb.DEBUG[2024-07-06 16:01:39.231][self$set] Set key compute.fields to TRUE. biodb.DEBUG[2024-07-06 16:01:39.231][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.234][self$getConfig()$define] Define config key factory.cache. biodb.DEBUG[2024-07-06 16:01:39.235][self$getConfig()$define] Define config key force.locale. biodb.DEBUG[2024-07-06 16:01:39.236][self$set] Set key force.locale to TRUE. biodb.DEBUG[2024-07-06 16:01:39.237][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.240][self$getConfig()$define] Define config key longterm.cache.subfolder. biodb.DEBUG[2024-07-06 16:01:39.241][self$getConfig()$define] Define config key msg.caution.lvl. biodb.DEBUG[2024-07-06 16:01:39.242][self$getConfig()$define] Define config key msg.debug.lvl. biodb.DEBUG[2024-07-06 16:01:39.243][self$getConfig()$define] Define config key msg.info.lvl. biodb.DEBUG[2024-07-06 16:01:39.244][self$getConfig()$define] Define config key multival.field.sep. biodb.DEBUG[2024-07-06 16:01:39.245][self$set] Set key multival.field.sep to ";". biodb.DEBUG[2024-07-06 16:01:39.246][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.249][self$getConfig()$define] Define config key intra.field.name.sep. biodb.DEBUG[2024-07-06 16:01:39.250][self$set] Set key intra.field.name.sep to ".". biodb.DEBUG[2024-07-06 16:01:39.251][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.254][self$getConfig()$define] Define config key entries.sep. biodb.DEBUG[2024-07-06 16:01:39.255][self$set] Set key entries.sep to "|". biodb.DEBUG[2024-07-06 16:01:39.255][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.258][self$getConfig()$define] Define config key offline. biodb.DEBUG[2024-07-06 16:01:39.259][self$set] Set key offline to FALSE. biodb.DEBUG[2024-07-06 16:01:39.260][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.263][self$getConfig()$define] Define config key persistent.cache.impl. biodb.DEBUG[2024-07-06 16:01:39.264][self$set] Set key persistent.cache.impl to "custom". biodb.DEBUG[2024-07-06 16:01:39.265][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.268][self$getConfig()$define] Define config key proton.mass. biodb.DEBUG[2024-07-06 16:01:39.269][self$set] Set key proton.mass to 1.0072765. biodb.DEBUG[2024-07-06 16:01:39.270][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.272][self$getConfig()$define] Define config key shortterm.cache.subfolder. biodb.DEBUG[2024-07-06 16:01:39.273][self$getConfig()$define] Define config key svn.binary.path. biodb.DEBUG[2024-07-06 16:01:39.278][self$set] Set key svn.binary.path to "". biodb.DEBUG[2024-07-06 16:01:39.279][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.281][self$getConfig()$define] Define config key test.functions. biodb.DEBUG[2024-07-06 16:01:39.283][self$getConfig()$define] Define config key useragent. biodb.DEBUG[2024-07-06 16:01:39.284][self$set] Set key useragent to "R Bioconductor biodb library.". biodb.DEBUG[2024-07-06 16:01:39.284][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.290][self$getDbsInfo()$define] Define connector comp.csv.file. biodb.DEBUG[2024-07-06 16:01:39.327][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-07-06 16:01:39.350][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.". biodb.DEBUG[2024-07-06 16:01:39.351][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.352][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-07-06 16:01:39.353][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.354][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-07-06 16:01:39.354][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-07-06 16:01:39.355][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-07-06 16:01:39.356][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-07-06 16:01:39.357][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-07-06 16:01:39.358][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.359][self$setPropertyValue] Setting property "name" to "Compound CSV File". biodb.DEBUG[2024-07-06 16:01:39.360][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-07-06 16:01:39.361][self$setPropertyValue] biodb.DEBUG[2024-07-06 16:01:39.362][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.362][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-07-06 16:01:39.362][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-07-06 16:01:39.362][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-07-06 16:01:39.362][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-07-06 16:01:39.362][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-07-06 16:01:39.363][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-07-06 16:01:39.364][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-07-06 16:01:39.365][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-07-06 16:01:39.366][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-07-06 16:01:39.367][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-07-06 16:01:39.368][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-07-06 16:01:39.368][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-07-06 16:01:39.369][self$setPropertyValue] biodb.DEBUG[2024-07-06 16:01:39.370][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-07-06 16:01:39.371][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-07-06 16:01:39.372][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-07-06 16:01:39.373][self$setPropertyValue] biodb.DEBUG[2024-07-06 16:01:39.374][self$getDbsInfo()$define] Define connector comp.sqlite. biodb.DEBUG[2024-07-06 16:01:39.375][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-07-06 16:01:39.376][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.". biodb.DEBUG[2024-07-06 16:01:39.377][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.378][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-07-06 16:01:39.379][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.380][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-07-06 16:01:39.381][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-07-06 16:01:39.382][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-07-06 16:01:39.383][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-07-06 16:01:39.384][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-07-06 16:01:39.384][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.385][self$setPropertyValue] Setting property "name" to "Compound SQLite". biodb.DEBUG[2024-07-06 16:01:39.386][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-07-06 16:01:39.387][self$setPropertyValue] biodb.DEBUG[2024-07-06 16:01:39.388][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.389][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-07-06 16:01:39.389][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-07-06 16:01:39.389][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-07-06 16:01:39.389][self$setPropertyValue] Setting property "searchable.fields" to "average.mass". biodb.DEBUG[2024-07-06 16:01:39.389][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass". biodb.DEBUG[2024-07-06 16:01:39.390][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-07-06 16:01:39.391][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-07-06 16:01:39.391][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-07-06 16:01:39.392][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-07-06 16:01:39.393][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-07-06 16:01:39.394][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-07-06 16:01:39.395][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-07-06 16:01:39.396][self$setPropertyValue] biodb.DEBUG[2024-07-06 16:01:39.397][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-07-06 16:01:39.397][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-07-06 16:01:39.398][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-07-06 16:01:39.399][self$setPropertyValue] biodb.DEBUG[2024-07-06 16:01:39.400][self$getDbsInfo()$define] Define connector mass.csv.file. biodb.DEBUG[2024-07-06 16:01:39.402][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.403][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..". biodb.DEBUG[2024-07-06 16:01:39.404][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.405][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-07-06 16:01:39.405][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.406][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-07-06 16:01:39.407][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-07-06 16:01:39.408][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-07-06 16:01:39.409][self$setPropertyValue] Setting property "entry.content.type" to "tsv". biodb.DEBUG[2024-07-06 16:01:39.410][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-07-06 16:01:39.411][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-07-06 16:01:39.412][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File". biodb.DEBUG[2024-07-06 16:01:39.413][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-07-06 16:01:39.413][self$setPropertyValue] biodb.DEBUG[2024-07-06 16:01:39.414][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.415][self$setPropertyValue] biodb.DEBUG[2024-07-06 16:01:39.416][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-07-06 16:01:39.417][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-07-06 16:01:39.418][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-07-06 16:01:39.419][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-07-06 16:01:39.419][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-07-06 16:01:39.420][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-07-06 16:01:39.421][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-07-06 16:01:39.422][self$setPropertyValue] biodb.DEBUG[2024-07-06 16:01:39.423][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-07-06 16:01:39.424][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-07-06 16:01:39.425][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-07-06 16:01:39.425][self$setPropertyValue] biodb.DEBUG[2024-07-06 16:01:39.426][self$getDbsInfo()$define] Define connector mass.sqlite. biodb.DEBUG[2024-07-06 16:01:39.428][self$setPropertyValue] Setting property "compound.db" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.429][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.". biodb.DEBUG[2024-07-06 16:01:39.430][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.431][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-07-06 16:01:39.432][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.433][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-07-06 16:01:39.433][self$setPropertyValue] Setting property "editable" to "TRUE". biodb.DEBUG[2024-07-06 16:01:39.434][self$setPropertyValue] Setting property "entry.content.encoding" to "NA". biodb.DEBUG[2024-07-06 16:01:39.435][self$setPropertyValue] Setting property "entry.content.type" to "list". biodb.DEBUG[2024-07-06 16:01:39.440][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-07-06 16:01:39.442][self$setPropertyValue] Setting property "mass.db" to "TRUE". biodb.DEBUG[2024-07-06 16:01:39.443][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite". biodb.DEBUG[2024-07-06 16:01:39.444][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-07-06 16:01:39.445][self$setPropertyValue] biodb.DEBUG[2024-07-06 16:01:39.446][self$setPropertyValue] Setting property "remote" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.447][self$setPropertyValue] biodb.DEBUG[2024-07-06 16:01:39.448][self$setPropertyValue] Setting property "scheduler.n" to "1". biodb.DEBUG[2024-07-06 16:01:39.449][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-07-06 16:01:39.450][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-07-06 16:01:39.451][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-07-06 16:01:39.452][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-07-06 16:01:39.453][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-07-06 16:01:39.454][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-07-06 16:01:39.455][self$setPropertyValue] biodb.DEBUG[2024-07-06 16:01:39.456][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-07-06 16:01:39.457][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-07-06 16:01:39.457][self$setPropertyValue] Setting property "writable" to "TRUE". biodb.DEBUG[2024-07-06 16:01:39.458][self$setPropertyValue] biodb.DEBUG[2024-07-06 16:01:39.464][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-07-06 16:01:39.464][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.466][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.471][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.473][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.475][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.476][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.479][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.484][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.485][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.486][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.488][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.493][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.497][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.501][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.502][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.504][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.506][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.507][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.510][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.514][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.515][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.519][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.523][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.527][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.532][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.536][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.540][self$getEntryFields()$define] Define field accession. biodb.DEBUG[2024-07-06 16:01:39.546][self$getEntryFields()$define] Define field description. biodb.DEBUG[2024-07-06 16:01:39.547][self$getEntryFields()$define] Define field name. biodb.DEBUG[2024-07-06 16:01:39.549][self$getEntryFields()$define] Define field cas.id. biodb.DEBUG[2024-07-06 16:01:39.550][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-07-06 16:01:39.552][self$getEntryFields()$define] Define field chemspider.id. biodb.DEBUG[2024-07-06 16:01:39.553][self$getEntryFields()$define] Define field comp.csv.file.id. biodb.DEBUG[2024-07-06 16:01:39.554][self$getEntryFields()$define] Define field comp.sqlite.id. biodb.DEBUG[2024-07-06 16:01:39.556][self$getEntryFields()$define] Define field expasy.enzyme.id. biodb.DEBUG[2024-07-06 16:01:39.557][self$getEntryFields()$define] Define field hmdb.metabolites.id. biodb.DEBUG[2024-07-06 16:01:39.558][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-07-06 16:01:39.560][self$getEntryFields()$define] Define field kegg.genes.id. biodb.DEBUG[2024-07-06 16:01:39.561][self$getEntryFields()$define] Define field mass.csv.file.id. biodb.DEBUG[2024-07-06 16:01:39.562][self$getEntryFields()$define] Define field mass.sqlite.id. biodb.DEBUG[2024-07-06 16:01:39.564][self$getEntryFields()$define] Define field ncbi.gene.id. biodb.DEBUG[2024-07-06 16:01:39.565][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id. biodb.DEBUG[2024-07-06 16:01:39.567][self$getEntryFields()$define] Define field compound.id. biodb.DEBUG[2024-07-06 16:01:39.568][self$getEntryFields()$define] Define field average.mass. biodb.DEBUG[2024-07-06 16:01:39.569][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-07-06 16:01:39.571][self$getEntryFields()$define] Define field monoisotopic.mass. biodb.DEBUG[2024-07-06 16:01:39.572][self$getEntryFields()$define] Define field nominal.mass. biodb.DEBUG[2024-07-06 16:01:39.573][self$getEntryFields()$define] Define field peak.attr. biodb.DEBUG[2024-07-06 16:01:39.575][self$getEntryFields()$define] Define field peak.comp. biodb.DEBUG[2024-07-06 16:01:39.576][self$getEntryFields()$define] Define field peak.error.ppm. biodb.DEBUG[2024-07-06 16:01:39.577][self$getEntryFields()$define] Define field peak.formula. biodb.DEBUG[2024-07-06 16:01:39.579][self$getEntryFields()$define] Define field peak.intensity. biodb.DEBUG[2024-07-06 16:01:39.580][self$getEntryFields()$define] Define field peak.mass. biodb.DEBUG[2024-07-06 16:01:39.582][self$getEntryFields()$define] Define field peak.mztheo. biodb.DEBUG[2024-07-06 16:01:39.583][self$getEntryFields()$define] Define field peak.mzexp. biodb.DEBUG[2024-07-06 16:01:39.584][self$getEntryFields()$define] Define field peak.mz. biodb.DEBUG[2024-07-06 16:01:39.586][self$getEntryFields()$define] Define field peak.relative.intensity. biodb.DEBUG[2024-07-06 16:01:39.587][self$getEntryFields()$define] Define field peaks. biodb.DEBUG[2024-07-06 16:01:39.588][self$getEntryFields()$define] Define field chrom.col.constructor. biodb.DEBUG[2024-07-06 16:01:39.590][self$getEntryFields()$define] Define field chrom.col.diameter. biodb.DEBUG[2024-07-06 16:01:39.591][self$getEntryFields()$define] Define field chrom.col.id. biodb.DEBUG[2024-07-06 16:01:39.592][self$getEntryFields()$define] Define field chrom.col.length. biodb.DEBUG[2024-07-06 16:01:39.606][self$getEntryFields()$define] Define field chrom.col.method.protocol. biodb.DEBUG[2024-07-06 16:01:39.607][self$getEntryFields()$define] Define field chrom.col.name. biodb.DEBUG[2024-07-06 16:01:39.609][self$getEntryFields()$define] Define field chrom.flow.gradient. biodb.DEBUG[2024-07-06 16:01:39.610][self$getEntryFields()$define] Define field chrom.flow.rate. biodb.DEBUG[2024-07-06 16:01:39.611][self$getEntryFields()$define] Define field chrom.rt. biodb.DEBUG[2024-07-06 16:01:39.613][self$getEntryFields()$define] Define field chrom.rt.max. biodb.DEBUG[2024-07-06 16:01:39.614][self$getEntryFields()$define] Define field chrom.rt.min. biodb.DEBUG[2024-07-06 16:01:39.616][self$getEntryFields()$define] Define field chrom.rt.unit. biodb.DEBUG[2024-07-06 16:01:39.617][self$getEntryFields()$define] Define field chrom.solvent. biodb.DEBUG[2024-07-06 16:01:39.618][self$getEntryFields()$define] Define field aa.seq. biodb.DEBUG[2024-07-06 16:01:39.620][self$getEntryFields()$define] Define field aa.seq.length. biodb.DEBUG[2024-07-06 16:01:39.621][self$getEntryFields()$define] Define field aa.seq.location. biodb.DEBUG[2024-07-06 16:01:39.623][self$getEntryFields()$define] Define field nt.seq. biodb.DEBUG[2024-07-06 16:01:39.624][self$getEntryFields()$define] Define field nt.seq.length. biodb.DEBUG[2024-07-06 16:01:39.625][self$getEntryFields()$define] Define field ec. biodb.DEBUG[2024-07-06 16:01:39.627][self$getEntryFields()$define] Define field organism. biodb.DEBUG[2024-07-06 16:01:39.628][self$getEntryFields()$define] Define field pathway.class. biodb.DEBUG[2024-07-06 16:01:39.629][self$getEntryFields()$define] Define field catalytic.activity. biodb.DEBUG[2024-07-06 16:01:39.631][self$getEntryFields()$define] Define field cofactor. biodb.DEBUG[2024-07-06 16:01:39.632][self$getEntryFields()$define] Define field gene.symbol. biodb.DEBUG[2024-07-06 16:01:39.634][self$getEntryFields()$define] Define field charge. biodb.DEBUG[2024-07-06 16:01:39.635][self$getEntryFields()$define] Define field comp.iupac.name.allowed. biodb.DEBUG[2024-07-06 16:01:39.636][self$getEntryFields()$define] Define field comp.iupac.name.cas. biodb.DEBUG[2024-07-06 16:01:39.638][self$getEntryFields()$define] Define field comp.iupac.name.pref. biodb.DEBUG[2024-07-06 16:01:39.639][self$getEntryFields()$define] Define field comp.iupac.name.syst. biodb.DEBUG[2024-07-06 16:01:39.641][self$getEntryFields()$define] Define field comp.iupac.name.trad. biodb.DEBUG[2024-07-06 16:01:39.642][self$getEntryFields()$define] Define field comp.super.class. biodb.DEBUG[2024-07-06 16:01:39.643][self$getEntryFields()$define] Define field equation. biodb.DEBUG[2024-07-06 16:01:39.645][self$getEntryFields()$define] Define field formula. biodb.DEBUG[2024-07-06 16:01:39.646][self$getEntryFields()$define] Define field composition. biodb.DEBUG[2024-07-06 16:01:39.648][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-07-06 16:01:39.649][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-07-06 16:01:39.650][self$getEntryFields()$define] Define field logp. biodb.DEBUG[2024-07-06 16:01:39.652][self$getEntryFields()$define] Define field ms.level. biodb.DEBUG[2024-07-06 16:01:39.653][self$getEntryFields()$define] Define field ms.mode. biodb.DEBUG[2024-07-06 16:01:39.654][self$getEntryFields()$define] Define field msdev. biodb.DEBUG[2024-07-06 16:01:39.656][self$getEntryFields()$define] Define field msdevtype. biodb.DEBUG[2024-07-06 16:01:39.657][self$getEntryFields()$define] Define field msprecannot. biodb.DEBUG[2024-07-06 16:01:39.658][self$getEntryFields()$define] Define field msprecmz. biodb.DEBUG[2024-07-06 16:01:39.660][self$getEntryFields()$define] Define field mstype. biodb.DEBUG[2024-07-06 16:01:39.661][self$getEntryFields()$define] Define field nb.compounds. biodb.DEBUG[2024-07-06 16:01:39.663][self$getEntryFields()$define] Define field nb.peaks. biodb.DEBUG[2024-07-06 16:01:39.664][self$getEntryFields()$define] Define field products. biodb.DEBUG[2024-07-06 16:01:39.665][self$getEntryFields()$define] Define field smiles. biodb.DEBUG[2024-07-06 16:01:39.667][self$getEntryFields()$define] Define field smiles.canonical. biodb.DEBUG[2024-07-06 16:01:39.668][self$getEntryFields()$define] Define field smiles.isomeric. biodb.DEBUG[2024-07-06 16:01:39.669][self$getEntryFields()$define] Define field substrates. biodb.DEBUG[2024-07-06 16:01:39.676][initialize] Created successfully new BiodbMain instance. biodb.DEBUG[2024-07-06 16:01:39.677][initialize] This is biodb version 1.13.0. biodb.DEBUG[2024-07-06 16:01:39.681][notifyObservers] Notify observers for notifyNewObservers. biodb.DEBUG[2024-07-06 16:01:39.681][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.683][FUN] Trying to call function notifyNewObservers on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.689][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.693][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.695][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.700][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.701][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.707][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.712][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.714][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.718][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.723][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.729][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.734][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.740][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.741][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.745][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.751][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.757][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.758][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.762][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.768][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.773][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.779][notifyObservers] Notify observers for notifyCfgUpdate. biodb.DEBUG[2024-07-06 16:01:39.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.784][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:39.785][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbChebi.Rcheck/biodbChebi/definitions.yml". biodb.DEBUG[2024-07-06 16:01:39.795][self$getDbsInfo()$define] Define connector chebi. biodb.DEBUG[2024-07-06 16:01:39.796][self$setPropertyValue] Setting property "compound.db" to "TRUE". biodb.DEBUG[2024-07-06 16:01:39.797][self$setPropertyValue] Setting property "description" to "NA". biodb.DEBUG[2024-07-06 16:01:39.798][self$setPropertyValue] Setting property "disabled" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.799][self$setPropertyValue] Setting property "disabling.reason" to "". biodb.DEBUG[2024-07-06 16:01:39.800][self$setPropertyValue] Setting property "downloadable" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.801][self$setPropertyValue] Setting property "dwnld.ext" to "NA". biodb.DEBUG[2024-07-06 16:01:39.802][self$setPropertyValue] Setting property "editable" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.803][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8". biodb.DEBUG[2024-07-06 16:01:39.804][self$setPropertyValue] Setting property "entry.content.type" to "xml". biodb.DEBUG[2024-07-06 16:01:39.805][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")". biodb.DEBUG[2024-07-06 16:01:39.806][self$setPropertyValue] Setting property "mass.db" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.807][self$setPropertyValue] Setting property "name" to "ChEBI". biodb.DEBUG[2024-07-06 16:01:39.807][self$setPropertyValue] Setting property "package" to "biodb". biodb.DEBUG[2024-07-06 16:01:39.808][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')". biodb.DEBUG[2024-07-06 16:01:39.808][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge". biodb.DEBUG[2024-07-06 16:01:39.808][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")". biodb.DEBUG[2024-07-06 16:01:39.808][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi". biodb.DEBUG[2024-07-06 16:01:39.808][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey". biodb.DEBUG[2024-07-06 16:01:39.808][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data". biodb.DEBUG[2024-07-06 16:01:39.808][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass". biodb.DEBUG[2024-07-06 16:01:39.808][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass". biodb.DEBUG[2024-07-06 16:01:39.808][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")". biodb.DEBUG[2024-07-06 16:01:39.808][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar". biodb.DEBUG[2024-07-06 16:01:39.808][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles". biodb.DEBUG[2024-07-06 16:01:39.809][self$setPropertyValue] Setting property "remote" to "TRUE". biodb.DEBUG[2024-07-06 16:01:39.810][self$setPropertyValue] Setting property "searchable.fields" to "name". biodb.DEBUG[2024-07-06 16:01:39.810][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass". biodb.DEBUG[2024-07-06 16:01:39.810][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass". biodb.DEBUG[2024-07-06 16:01:39.811][self$setPropertyValue] Setting property "scheduler.n" to "3". biodb.DEBUG[2024-07-06 16:01:39.812][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-07-06 16:01:39.813][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-07-06 16:01:39.814][self$setPropertyValue] Setting property "scheduler.t" to "1". biodb.DEBUG[2024-07-06 16:01:39.815][self$setPropertyValue] Notifying observers about frequency change. biodb.DEBUG[2024-07-06 16:01:39.815][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated. biodb.DEBUG[2024-07-06 16:01:39.816][self$setPropertyValue] Setting property "token" to "NA". biodb.DEBUG[2024-07-06 16:01:39.817][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:01:39.817][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/". biodb.DEBUG[2024-07-06 16:01:39.818][self$setPropertyValue] Notifying observers about URLs change. biodb.DEBUG[2024-07-06 16:01:39.819][notifyObservers] Notify observers for notifyConnUrlsUpdated. biodb.DEBUG[2024-07-06 16:01:39.820][self$setPropertyValue] Setting property "writable" to "FALSE". biodb.DEBUG[2024-07-06 16:01:39.821][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi". biodb.DEBUG[2024-07-06 16:01:39.821][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema". biodb.DEBUG[2024-07-06 16:01:39.826][self$getEntryFields()$define] Define field chebi.id. biodb.DEBUG[2024-07-06 16:01:39.828][self$getEntryFields()$define] Define field kegg.compound.id. biodb.DEBUG[2024-07-06 16:01:39.829][self$getEntryFields()$define] Define field n_stars. biodb.DEBUG[2024-07-06 16:01:39.831][self$getEntryFields()$define] Define field molecular.mass. biodb.DEBUG[2024-07-06 16:01:39.832][self$getEntryFields()$define] Define field inchi. biodb.DEBUG[2024-07-06 16:01:39.833][self$getEntryFields()$define] Define field inchikey. biodb.DEBUG[2024-07-06 16:01:39.861][super$initialize] Initialize connector chebi. biodb.DEBUG[2024-07-06 16:01:39.863][super$initialize] Register connector chebi with the request scheduler biodb.DEBUG[2024-07-06 16:01:39.867][private$bdb$getRequestScheduler()$re ...] Register connector chebi. biodb.DEBUG[2024-07-06 16:01:39.871][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi". biodb.DEBUG[2024-07-06 16:01:39.876][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-07-06 16:01:39.877][self$setFrequency] t=1.000000, n=3.000000 biodb.DEBUG[2024-07-06 16:01:39.878][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk". biodb.DEBUG[2024-07-06 16:01:39.879][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi . biodb.INFO [2024-07-06 16:01:39.888][biodb::testThat] biodb.INFO [2024-07-06 16:01:39.889][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value "). biodb.INFO [2024-07-06 16:01:39.890][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-07-06 16:01:39.891][biodb::testThat] biodb.TRACE[2024-07-06 16:01:39.895][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbChebi.Rcheck/biodbChebi/testref/entry-chebi-15440-content.xml". biodb.DEBUG[2024-07-06 16:01:39.896][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:39.900][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:39.909][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:39.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:39.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:39.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:39.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:39.925][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:39.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:39.936][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:39.937][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:39.938][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:39.939][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:39.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:39.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:39.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:39.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:39.955][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:39.956][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:39.957][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:39.958][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:39.983][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:39.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:39.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:39.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:39.987][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:39.988][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:39.989][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:39.990][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:39.991][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:39.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:39.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:39.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:39.995][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:39.995][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:39.996][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:39.997][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:39.998][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:39.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:40.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.002][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:40.003][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:40.004][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.005][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:40.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:40.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.010][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.011][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.012][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.012][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.014][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.017][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:40.018][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.019][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.020][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.021][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:40.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.025][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.026][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.027][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.028][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.032][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:40.033][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:40.034][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.035][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.037][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:40.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:40.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.040][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:40.041][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:40.042][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.043][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.044][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:40.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:40.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.048][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:40.049][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:40.050][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.050][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.052][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:40.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:40.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.069][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:40.131][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440. biodb.TRACE[2024-07-06 16:01:40.133][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:40.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:40.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.137][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:40.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:40.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.161][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:40.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:40.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.165][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:40.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:40.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.176][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-07-06 16:01:40.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-07-06 16:01:40.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.179][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-07-06 16:01:40.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-07-06 16:01:40.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.183][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-07-06 16:01:40.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-07-06 16:01:40.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.186][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-07-06 16:01:40.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-07-06 16:01:40.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.242][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.256][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.269][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.276][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.277][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.278][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.279][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.317][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.323][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.324][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.325][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.326][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.327][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.338][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:40.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:40.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.342][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:40.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:40.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.345][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:40.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:40.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.349][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:40.350][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:40.351][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.352][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.352][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:40.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:40.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.362][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:40.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:40.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.366][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:40.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:40.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.370][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:40.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:40.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.373][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:40.374][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:40.375][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.376][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.377][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:40.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:40.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.387][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.398][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.399][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.399][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.400][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.411][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.418][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.421][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.422][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.423][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.424][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.425][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.435][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:40.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:40.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.439][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:40.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:40.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.442][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:40.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:40.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.446][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:40.447][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:40.448][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.449][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.450][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:40.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:40.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.460][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:40.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:40.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.462][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.463][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:40.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:40.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.466][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.467][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:40.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:40.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.470][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:40.471][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:40.472][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.473][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.474][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:40.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:40.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.484][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.486][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.487][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.491][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.494][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.494][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.495][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.496][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.497][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.498][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.508][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:40.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:40.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.511][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.512][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:40.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:40.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.520][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:40.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:40.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.523][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:40.524][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:40.525][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.526][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.527][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:40.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:40.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.529][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:40.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:40.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:40.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:40.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:40.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:40.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.548][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:40.549][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:40.550][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.550][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.551][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:40.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:40.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.561][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:40.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:40.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.564][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.565][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:40.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:40.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:40.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:40.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.572][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:40.573][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:40.574][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.575][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.576][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:40.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:40.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.578][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.586][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.587][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.587][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.588][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.592][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:40.593][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:40.594][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.595][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.598][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:40.599][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:40.600][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.601][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.605][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:40.606][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:40.607][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.607][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.611][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:40.612][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:40.613][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.614][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.617][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.618][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.619][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.620][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.624][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.625][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.625][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.626][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.630][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.631][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.632][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.633][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.636][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:40.637][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:40.638][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.639][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.643][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:40.644][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:40.644][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.645][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.649][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:40.650][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:40.651][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.652][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.666][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbChebi.Rcheck/biodbChebi/testref/entry-chebi-2528-content.xml". biodb.DEBUG[2024-07-06 16:01:40.698][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:40.700][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:40.701][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:40.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:40.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:40.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:40.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:40.712][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:40.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:40.715][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.716][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.717][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.718][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.738][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:40.739][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:40.740][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.741][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.742][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:40.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:40.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.746][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:40.747][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:40.747][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.748][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.750][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:40.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:40.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.754][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:40.755][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:40.755][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.756][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.757][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:40.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:40.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.761][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:40.762][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:40.763][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.764][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.765][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:40.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:40.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.768][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.769][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.770][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.771][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.772][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:40.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.776][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:40.777][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.778][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.778][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.780][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:40.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.783][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.784][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.785][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.786][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:40.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.790][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:40.791][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:40.792][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.793][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:40.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:40.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.798][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:40.799][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:40.800][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.801][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.802][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:40.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:40.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.804][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.805][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:40.806][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:40.807][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.808][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.809][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:40.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:40.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:40.848][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 2528. biodb.TRACE[2024-07-06 16:01:40.867][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:40.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:40.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.870][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:40.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:40.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.874][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:40.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:40.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.877][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:40.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:40.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.884][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:40.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.888][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-07-06 16:01:40.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-07-06 16:01:40.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.892][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-07-06 16:01:40.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-07-06 16:01:40.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.899][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-07-06 16:01:40.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-07-06 16:01:40.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.902][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.903][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-07-06 16:01:40.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-07-06 16:01:40.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.930][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.943][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.979][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.980][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.981][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.982][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:40.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:40.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:40.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:40.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:40.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.003][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.004][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.005][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.006][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.017][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:41.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:41.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:41.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:41.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.024][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:41.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:41.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.027][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:41.028][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:41.029][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.030][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.031][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:41.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:41.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.041][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:41.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:41.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.044][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:41.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:41.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.048][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:41.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:41.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.052][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:41.053][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:41.053][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.054][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.055][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:41.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:41.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.065][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:41.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.072][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.076][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:41.077][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.077][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.078][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.079][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:41.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.104][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.105][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.106][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.106][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.121][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.128][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.129][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.130][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.131][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.141][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:41.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:41.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.145][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:41.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:41.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.149][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:41.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:41.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.152][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:41.153][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:41.154][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.155][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.156][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:41.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:41.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.166][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:41.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:41.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.169][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:41.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:41.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.173][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:41.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:41.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.176][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:41.177][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:41.178][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.179][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.180][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:41.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:41.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.190][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.193][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.197][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.200][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.201][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.202][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.203][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.204][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.214][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:41.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:41.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.217][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:41.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:41.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.221][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:41.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:41.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.224][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.224][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:41.225][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:41.226][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.227][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.228][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:41.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:41.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.238][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:41.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:41.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:41.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:41.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:41.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:41.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.249][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:41.250][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:41.250][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.251][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.252][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:41.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:41.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.266][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.270][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.273][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.274][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.275][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.276][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.277][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.287][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.288][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.289][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.290][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.298][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:41.299][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:41.300][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.301][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.305][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:41.306][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:41.307][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.307][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.311][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.312][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.313][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.314][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.318][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:41.319][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:41.320][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.320][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.324][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.325][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.326][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.327][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.330][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.331][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.332][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.333][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.337][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.338][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.339][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.339][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.343][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:41.344][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:41.345][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.346][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.349][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:41.350][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:41.351][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.352][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.356][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:41.357][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:41.358][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.358][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.362][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbChebi.Rcheck/biodbChebi/testref/entry-chebi-7799-content.xml". biodb.DEBUG[2024-07-06 16:01:41.363][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:41.365][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:41.366][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:41.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:41.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:41.371][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:41.372][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:41.373][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:41.374][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:41.376][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.377][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.377][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.378][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.379][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.383][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:41.384][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:41.385][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.386][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.387][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:41.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:41.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.389][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.390][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:41.391][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:41.392][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.393][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.394][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:41.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:41.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.398][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.399][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.400][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.400][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.401][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.405][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:41.406][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:41.407][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.408][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.409][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:41.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:41.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.412][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.413][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.414][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.415][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.416][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.420][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:41.421][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.422][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.422][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.424][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:41.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.427][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.428][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.429][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.430][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.434][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:41.435][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:41.436][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.437][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.438][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:41.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:41.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.442][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:41.443][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:41.444][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.445][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.446][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:41.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:41.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.449][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:41.450][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:41.451][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.452][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.453][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:41.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:41.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.460][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.466][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.473][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.474][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.477][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.488][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.491][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:41.492][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 7799. biodb.TRACE[2024-07-06 16:01:41.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.502][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.505][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.506][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:41.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:41.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.509][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:41.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:41.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.516][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.520][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-07-06 16:01:41.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-07-06 16:01:41.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.523][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-07-06 16:01:41.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-07-06 16:01:41.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.527][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-07-06 16:01:41.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-07-06 16:01:41.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.531][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-07-06 16:01:41.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-07-06 16:01:41.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:41.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.589][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.590][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.594][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.596][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.597][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.598][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.599][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.600][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.611][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:41.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:41.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.614][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:41.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:41.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.618][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:41.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:41.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.621][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:41.622][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:41.623][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.624][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.625][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:41.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:41.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.635][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.638][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.642][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.645][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.646][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.647][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.647][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.648][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.649][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.659][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:41.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:41.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:41.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:41.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.666][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:41.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:41.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.670][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:41.671][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:41.672][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.673][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.674][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:41.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:41.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.684][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.687][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.691][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.699][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.700][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.701][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.702][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.702][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.715][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.716][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.720][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.723][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.724][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.725][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.726][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.730][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.737][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.740][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.748][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.749][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.750][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.751][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.762][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:41.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:41.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.765][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:41.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:41.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.769][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:41.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:41.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.772][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:41.773][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:41.774][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.775][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.776][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:41.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:41.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.786][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:41.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:41.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.789][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:41.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:41.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.793][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:41.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:41.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.797][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:41.797][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:41.798][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.799][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.800][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:41.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:41.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.810][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:41.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:41.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:41.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:41.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:41.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:41.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.820][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.821][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:41.822][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:41.823][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.824][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.824][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:41.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:41.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.835][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:41.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:41.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.838][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:41.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:41.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.842][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:41.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:41.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.845][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:41.846][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:41.847][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.848][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.849][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:41.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:41.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.859][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.860][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.861][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.862][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.865][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:41.866][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:41.867][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.868][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.872][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:41.873][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:41.874][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.874][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.878][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.879][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.880][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.881][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.885][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:41.886][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:41.887][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.887][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.891][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.892][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:41.893][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.894][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.902][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.903][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:41.904][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.905][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.909][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.910][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:41.910][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.911][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.915][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:01:41.916][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:41.917][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.918][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.922][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:41.923][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:41.923][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.924][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.928][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:41.929][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:41.930][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.931][ef$get] fields variable is a list. biodb.INFO [2024-07-06 16:01:41.937][biodb::testThat] biodb.INFO [2024-07-06 16:01:41.938][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. "). biodb.INFO [2024-07-06 16:01:41.938][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-07-06 16:01:41.939][biodb::testThat] biodb.DEBUG[2024-07-06 16:01:41.941][private$loadEntries] Creating entries from ids [3]: "15440, 2528, 7799". biodb.DEBUG[2024-07-06 16:01:41.948][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)... biodb.TRACE[2024-07-06 16:01:41.953][cch$loadFileContent] Trying to load 3 files from cache: [3]: "15440, 2528, 7799". biodb.TRACE[2024-07-06 16:01:41.954][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE". biodb.TRACE[2024-07-06 16:01:41.956][loadFileContents] Loaded 3 files from cache: [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml". biodb.DEBUG[2024-07-06 16:01:41.957][conn$getEntryContent] 3 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:41.958][self$createEntryFromContent] Creating ChEBI entries from 3 content(s). biodb.DEBUG[2024-07-06 16:01:41.959][self$createEntryFromContent] Parsing 3 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:41.961][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:41.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:41.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:41.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:41.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:41.968][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:41.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:41.971][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.972][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.973][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.974][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:41.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:41.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.977][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.978][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:41.979][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:41.980][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.981][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.982][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:41.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:41.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.986][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:41.987][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:41.988][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.989][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.990][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:41.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:41.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.993][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.994][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.995][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:41.996][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:41.997][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:41.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:41.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.001][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:42.002][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:42.003][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.004][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.005][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:42.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:42.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.008][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:42.009][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:42.010][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.011][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.012][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:42.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:42.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.016][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:42.017][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:42.018][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.018][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.020][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:42.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:42.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.023][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:42.024][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:42.025][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.026][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:42.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:42.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.031][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:42.032][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:42.032][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.033][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.035][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:42.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:42.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.038][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:42.039][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:42.040][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.041][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.042][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:42.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:42.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.046][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:42.047][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:42.047][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.048][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.049][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:42.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:42.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:42.078][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:42.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:42.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:42.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:42.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:42.085][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:42.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:42.089][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.090][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.090][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.091][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.096][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:42.097][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:42.098][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.099][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.100][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:42.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:42.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.103][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:42.110][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:42.110][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.111][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.113][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:42.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:42.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.116][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:42.117][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:42.118][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.119][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:42.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:42.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.124][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:42.125][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:42.126][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.127][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.128][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:42.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:42.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.131][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:42.132][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:42.133][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.134][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.135][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:42.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:42.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.139][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:42.140][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:42.141][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.142][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.143][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:42.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:42.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.147][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:42.147][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:42.148][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.149][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:42.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:42.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.154][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:42.155][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:42.156][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.157][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.158][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:42.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:42.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.162][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:42.163][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:42.163][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.164][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.165][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:42.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:42.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.169][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:42.170][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:42.171][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.172][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.173][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:42.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:42.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.180][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.184][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.195][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.198][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:42.203][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:42.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:42.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:42.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:42.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:42.210][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:42.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:42.213][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.214][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.215][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.216][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.221][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:42.222][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:42.223][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.224][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.225][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:42.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:42.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.229][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:42.230][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:42.231][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.232][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.233][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:42.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:42.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.237][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:42.238][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:42.238][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.239][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.240][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:42.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:42.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.244][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:42.245][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:42.246][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.247][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.248][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:42.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:42.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.252][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:42.252][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:42.253][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.254][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.255][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:42.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:42.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.259][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:42.260][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:42.261][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.262][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.263][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:42.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:42.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.267][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:42.267][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:42.268][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.269][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:42.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:42.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.274][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:42.275][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:42.276][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.277][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.278][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:42.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:42.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.282][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:42.283][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:42.283][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.284][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.285][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:42.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:42.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.289][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:42.290][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:42.291][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.292][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.293][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:42.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:42.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.299][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.300][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:42.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.318][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:42.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:42.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:42.358][self$createEntryFromContent] Accession numbers: 15440, 2528, 7799. biodb.TRACE[2024-07-06 16:01:42.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-07-06 16:01:42.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-07-06 16:01:42.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-07-06 16:01:42.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-07-06 16:01:42.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-07-06 16:01:42.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-07-06 16:01:42.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-07-06 16:01:42.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-07-06 16:01:42.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-07-06 16:01:42.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-07-06 16:01:42.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-07-06 16:01:42.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-07-06 16:01:42.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt. biodb.TRACE[2024-07-06 16:01:42.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt. biodb.TRACE[2024-07-06 16:01:42.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.389][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min. biodb.TRACE[2024-07-06 16:01:42.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min. biodb.TRACE[2024-07-06 16:01:42.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max. biodb.TRACE[2024-07-06 16:01:42.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max. biodb.TRACE[2024-07-06 16:01:42.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-07-06 16:01:42.403][biodb::testThat] biodb.INFO [2024-07-06 16:01:42.404][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field "). biodb.INFO [2024-07-06 16:01:42.404][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-07-06 16:01:42.405][biodb::testThat] biodb.TRACE[2024-07-06 16:01:42.408][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:42.409][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:42.410][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.411][ef$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:42.412][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name". biodb.TRACE[2024-07-06 16:01:42.433][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:42.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:42.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.437][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:42.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:42.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.440][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:42.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:42.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:42.446][function(conn, opt)] With value "squalene". biodb.DEBUG[2024-07-06 16:01:42.451][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl". biodb.DEBUG[2024-07-06 16:01:42.469][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:01:42.483][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05". biodb.TRACE[2024-07-06 16:01:42.484][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:42.486][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content". biodb.DEBUG[2024-07-06 16:01:42.511][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:01:42.514][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:01:42.515][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-07-06 16:01:42.516][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:42.518][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2024-07-06 16:01:42.519][function(conn, opt)] With found IDs [1]: "15440". biodb.TRACE[2024-07-06 16:01:42.529][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:42.530][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:42.531][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.532][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.533][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:42.533][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:42.534][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.535][ef$get] fields variable is a list. biodb.INFO [2024-07-06 16:01:42.539][biodb::testThat] biodb.INFO [2024-07-06 16:01:42.539][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. "). biodb.INFO [2024-07-06 16:01:42.540][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-07-06 16:01:42.541][biodb::testThat] biodb.TRACE[2024-07-06 16:01:42.562][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:42.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:42.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.564][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.565][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:42.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:42.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:42.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:42.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:42.621][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:01:42.624][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:01:42.626][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-07-06 16:01:42.627][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:42.628][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.INFO [2024-07-06 16:01:42.641][biodb::testThat] biodb.INFO [2024-07-06 16:01:42.642][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. "). biodb.INFO [2024-07-06 16:01:42.642][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-07-06 16:01:42.643][biodb::testThat] biodb.TRACE[2024-07-06 16:01:42.651][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:42.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:42.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.655][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:42.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:42.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.657][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:42.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:42.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.661][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.662][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:42.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:42.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:42.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:42.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.669][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:42.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:42.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.677][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-07-06 16:01:42.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-07-06 16:01:42.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.681][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-07-06 16:01:42.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-07-06 16:01:42.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.685][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-07-06 16:01:42.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-07-06 16:01:42.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.688][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-07-06 16:01:42.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-07-06 16:01:42.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.700][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:42.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:42.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.704][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:42.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:42.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.707][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:42.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:42.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.711][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:42.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:42.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:42.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:42.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.718][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:42.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:42.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.722][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-07-06 16:01:42.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-07-06 16:01:42.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.725][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz. biodb.TRACE[2024-07-06 16:01:42.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz. biodb.TRACE[2024-07-06 16:01:42.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.729][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp. biodb.TRACE[2024-07-06 16:01:42.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp. biodb.TRACE[2024-07-06 16:01:42.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:42.732][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo. biodb.TRACE[2024-07-06 16:01:42.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo. biodb.TRACE[2024-07-06 16:01:42.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:42.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-07-06 16:01:42.741][biodb::testThat] biodb.INFO [2024-07-06 16:01:42.741][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. "). biodb.INFO [2024-07-06 16:01:42.742][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-07-06 16:01:42.743][biodb::testThat] biodb.INFO [2024-07-06 16:01:42.751][biodb::testThat] biodb.INFO [2024-07-06 16:01:42.751][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. "). biodb.INFO [2024-07-06 16:01:42.752][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-07-06 16:01:42.753][biodb::testThat] biodb.INFO [2024-07-06 16:01:42.761][biodb::testThat] biodb.INFO [2024-07-06 16:01:42.762][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. "). biodb.INFO [2024-07-06 16:01:42.763][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-07-06 16:01:42.764][biodb::testThat] biodb.DEBUG[2024-07-06 16:01:42.767][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440". biodb.DEBUG[2024-07-06 16:01:43.841][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440. biodb.INFO [2024-07-06 16:01:45.245][biodb::testThat] biodb.INFO [2024-07-06 16:01:45.248][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. "). biodb.INFO [2024-07-06 16:01:45.250][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-07-06 16:01:45.252][biodb::testThat] biodb.DEBUG[2024-07-06 16:01:45.719][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400. biodb.TRACE[2024-07-06 16:01:46.190][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:46.192][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:46.194][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.196][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.198][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:46.201][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:46.203][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.205][ef$get] fields variable is a list. biodb.INFO [2024-07-06 16:01:46.209][biodb::testThat] biodb.INFO [2024-07-06 16:01:46.211][biodb::testThat] Running test function test.searchCompound (" We can search for a compound "). biodb.INFO [2024-07-06 16:01:46.213][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-07-06 16:01:46.215][biodb::testThat] biodb.TRACE[2024-07-06 16:01:46.234][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:46.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:46.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.239][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.240][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:46.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:46.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.246][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:46.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:46.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:46.327][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:01:46.330][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:01:46.331][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-07-06 16:01:46.332][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:46.333][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2024-07-06 16:01:46.424][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:01:46.428][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:01:46.429][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-07-06 16:01:46.431][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:46.432][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.TRACE[2024-07-06 16:01:46.445][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-07-06 16:01:46.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-07-06 16:01:46.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:46.479][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:01:46.482][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:01:46.483][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-07-06 16:01:46.485][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:46.486][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-07-06 16:01:46.489][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:46.490][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:46.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:46.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:46.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:46.497][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:46.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:46.499][private$loadEntries] Creating entries from ids [1]: "192288". biodb.DEBUG[2024-07-06 16:01:46.546][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:46.548][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288". biodb.TRACE[2024-07-06 16:01:46.549][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:46.550][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml". biodb.DEBUG[2024-07-06 16:01:46.552][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:46.553][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:46.554][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:46.555][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:46.556][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:46.557][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:46.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:46.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:46.568][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:46.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:46.571][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.572][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.573][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.574][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.578][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:46.579][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:46.580][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.581][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.582][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:46.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:46.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.586][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:46.587][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:46.588][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.589][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.590][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:46.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:46.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.594][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:46.595][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:46.596][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.597][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.598][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:46.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:46.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.601][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:46.602][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:46.603][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.604][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.605][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:46.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:46.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.609][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:46.610][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:46.611][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.611][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.613][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:46.614][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.614][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.615][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.616][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:46.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.620][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:46.621][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:46.622][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.623][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.624][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:46.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:46.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.626][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.627][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:46.628][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:46.629][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.630][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:46.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:46.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.635][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:46.636][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:46.637][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.638][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.639][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:46.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:46.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.642][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:46.643][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:46.644][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.645][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.646][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:46.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:46.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.649][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:46.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:46.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:46.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:46.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.656][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.657][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:46.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:46.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.663][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.671][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.674][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.675][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:46.686][self$createEntryFromContent] Accession numbers: 192288. biodb.TRACE[2024-07-06 16:01:46.695][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.702][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:46.706][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:01:46.709][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:01:46.710][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-07-06 16:01:46.711][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:46.713][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-07-06 16:01:46.731][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:46.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:46.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:46.737][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:46.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:46.739][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:46.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:46.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.744][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.748][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.751][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:46.752][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:46.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:46.753][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:46.757][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:46.758][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:46.759][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:46.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:46.761][private$loadEntries] Creating entries from ids [1]: "209892". biodb.DEBUG[2024-07-06 16:01:46.761][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:46.763][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892". biodb.TRACE[2024-07-06 16:01:46.764][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:46.765][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml". biodb.DEBUG[2024-07-06 16:01:46.766][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:46.767][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:46.768][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:46.770][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:46.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:46.772][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:46.776][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:46.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:46.777][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:46.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:46.780][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.781][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.782][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.783][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.787][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:46.788][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:46.789][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.790][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.791][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:46.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:46.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.795][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:46.796][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:46.797][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.798][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.799][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:46.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:46.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.803][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:46.804][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:46.804][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.805][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.806][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:46.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:46.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.810][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:46.811][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:46.812][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.813][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:46.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:46.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.818][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:46.819][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:46.819][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.820][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.821][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:46.822][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.823][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.824][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.825][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:46.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.829][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:46.830][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:46.831][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.832][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:46.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:46.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.836][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:46.837][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:46.838][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.839][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.840][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:46.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:46.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.844][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:46.845][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:46.846][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.847][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.848][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:46.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:46.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.851][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:46.852][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:46.853][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.854][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.855][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:46.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:46.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.859][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:46.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:46.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.863][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:46.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:46.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:46.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:46.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.876][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.889][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:46.900][self$createEntryFromContent] Accession numbers: 209892. biodb.TRACE[2024-07-06 16:01:46.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.905][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:46.927][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:01:46.930][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:01:46.931][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-07-06 16:01:46.932][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:46.933][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2024-07-06 16:01:46.936][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:46.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:46.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:46.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:46.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:46.943][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:46.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:46.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.948][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.952][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:46.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:46.955][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:46.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:46.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:46.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:46.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:46.962][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:46.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:46.964][private$loadEntries] Creating entries from ids [1]: "26747". biodb.DEBUG[2024-07-06 16:01:46.965][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:46.967][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747". biodb.TRACE[2024-07-06 16:01:46.968][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:46.969][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml". biodb.DEBUG[2024-07-06 16:01:46.970][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:46.971][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:46.972][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:46.974][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:46.975][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:46.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:46.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:46.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:46.981][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:46.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:46.984][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.985][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.986][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.987][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:46.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:46.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.992][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:46.992][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:46.993][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.994][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.995][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:46.996][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:46.997][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:46.998][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:46.999][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:47.000][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:47.001][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.002][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.003][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:47.004][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:47.005][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.006][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.007][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.008][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.008][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.009][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.010][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:47.011][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.012][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.013][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.014][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.015][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.016][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.017][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.018][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:47.019][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:47.020][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.021][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.022][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:47.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:47.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.025][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:47.026][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:47.027][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.028][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.029][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:47.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:47.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.033][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:47.034][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:47.035][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.035][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.069][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:47.077][self$createEntryFromContent] Accession numbers: 26747. biodb.TRACE[2024-07-06 16:01:47.078][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:47.096][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:47.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:47.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:47.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:47.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:47.104][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:47.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:47.106][private$loadEntries] Creating entries from ids [1]: "59285". biodb.DEBUG[2024-07-06 16:01:47.106][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:47.108][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285". biodb.TRACE[2024-07-06 16:01:47.109][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:47.110][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml". biodb.DEBUG[2024-07-06 16:01:47.111][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:47.113][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:47.114][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:47.115][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:47.116][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:47.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:47.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:47.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:47.122][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:47.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:47.125][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.126][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.127][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.128][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.133][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:47.134][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:47.135][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.136][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.137][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:47.138][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:47.139][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.139][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.141][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:47.142][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:47.142][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.143][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.144][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:47.145][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:47.146][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.147][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.148][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.149][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.150][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.151][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.152][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:47.153][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.154][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.155][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.156][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.157][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.157][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.158][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.159][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:47.160][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:47.161][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.162][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:47.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:47.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.167][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:47.168][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:47.169][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.170][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.171][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:47.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:47.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.175][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:47.176][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:47.176][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.177][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.193][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.197][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.200][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.203][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.204][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:47.219][self$createEntryFromContent] Accession numbers: 59285. biodb.TRACE[2024-07-06 16:01:47.220][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:47.239][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:47.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:47.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:47.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:47.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:47.246][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:47.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:47.248][private$loadEntries] Creating entries from ids [1]: "75174". biodb.DEBUG[2024-07-06 16:01:47.249][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:47.250][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174". biodb.TRACE[2024-07-06 16:01:47.251][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:47.253][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml". biodb.DEBUG[2024-07-06 16:01:47.254][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:47.255][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:47.256][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:47.257][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:47.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:47.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:47.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:47.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:47.265][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:47.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:47.267][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.268][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.269][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.270][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.275][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:47.276][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:47.277][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.278][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.279][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:47.280][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:47.281][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.281][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.283][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:47.284][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:47.285][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.285][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.287][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:47.288][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:47.288][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.289][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.290][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.291][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.292][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.293][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.294][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:47.295][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.296][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.297][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.298][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.299][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.300][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.301][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.302][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:47.303][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:47.304][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.304][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.306][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:47.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:47.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.309][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.310][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:47.311][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:47.312][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.312][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.314][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:47.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:47.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.316][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.317][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:47.318][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:47.319][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.320][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.327][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.332][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.346][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:47.357][self$createEntryFromContent] Accession numbers: 75174. biodb.TRACE[2024-07-06 16:01:47.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.365][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.373][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:47.380][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:47.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:47.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:47.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:47.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:47.388][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:47.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:47.390][private$loadEntries] Creating entries from ids [1]: "15441". biodb.DEBUG[2024-07-06 16:01:47.390][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:47.392][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441". biodb.TRACE[2024-07-06 16:01:47.393][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:47.395][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml". biodb.DEBUG[2024-07-06 16:01:47.396][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:47.397][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:47.398][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:47.399][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:47.400][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:47.401][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:47.405][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:47.406][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:47.406][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:47.407][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:47.409][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.410][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.411][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.412][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.416][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.417][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:47.418][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:47.418][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.419][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.420][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:47.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:47.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.424][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:47.425][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:47.426][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.427][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.428][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:47.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:47.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.432][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:47.433][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:47.433][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.434][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.435][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:47.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:47.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.439][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:47.440][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:47.441][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.442][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.443][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:47.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:47.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.446][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.447][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.448][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.449][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.450][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.454][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:47.455][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.456][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.457][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.458][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:47.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.461][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.462][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.463][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.464][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.469][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:47.470][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:47.471][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.471][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:47.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:47.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.477][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:47.478][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:47.478][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.479][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.480][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:47.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:47.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.484][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:47.485][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:47.486][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.487][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.488][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:47.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:47.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.494][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.505][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.509][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.517][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:47.527][self$createEntryFromContent] Accession numbers: 15441. biodb.TRACE[2024-07-06 16:01:47.528][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.558][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.564][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:47.565][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:47.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:47.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:47.571][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:47.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:47.572][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:47.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:47.574][private$loadEntries] Creating entries from ids [1]: "15442". biodb.DEBUG[2024-07-06 16:01:47.575][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:47.576][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442". biodb.TRACE[2024-07-06 16:01:47.578][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:47.579][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml". biodb.DEBUG[2024-07-06 16:01:47.580][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:47.581][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:47.582][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:47.584][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:47.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:47.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:47.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:47.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:47.591][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:47.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:47.594][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.595][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.596][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.596][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.601][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:47.602][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:47.603][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.604][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.605][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:47.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:47.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.609][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:47.610][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:47.611][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.611][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.613][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:47.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:47.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.616][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:47.617][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:47.618][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.619][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.620][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:47.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:47.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.624][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:47.625][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:47.626][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.626][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.628][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:47.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:47.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.631][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.632][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.633][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.634][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.635][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.639][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:47.640][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.640][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.641][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.642][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:47.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.645][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.646][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.647][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.648][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.649][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.650][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.654][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:47.654][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:47.655][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.656][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.657][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:47.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:47.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.661][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:47.662][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:47.663][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.664][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.665][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:47.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:47.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.668][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:47.669][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:47.670][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.671][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.672][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:47.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:47.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.679][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.680][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.693][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.694][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.698][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.702][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.705][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:47.713][self$createEntryFromContent] Accession numbers: 15442. biodb.TRACE[2024-07-06 16:01:47.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:47.729][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:47.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:47.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:47.735][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:47.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:47.737][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:47.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:47.738][private$loadEntries] Creating entries from ids [1]: "57310". biodb.DEBUG[2024-07-06 16:01:47.739][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:47.741][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310". biodb.TRACE[2024-07-06 16:01:47.742][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:47.743][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml". biodb.DEBUG[2024-07-06 16:01:47.745][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:47.746][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:47.747][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:47.748][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:47.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:47.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:47.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:47.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:47.756][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:47.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:47.759][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.760][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.761][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.761][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.763][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.766][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:47.767][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:47.768][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.769][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.770][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:47.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:47.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.774][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:47.775][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:47.776][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.776][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.778][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:47.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:47.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.781][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:47.782][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:47.783][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.784][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.785][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:47.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:47.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.789][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:47.790][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:47.791][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.791][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.793][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:47.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:47.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.796][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.797][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.798][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.799][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.800][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:47.801][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.802][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.803][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.804][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:47.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.808][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.809][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.809][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.810][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.815][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:47.816][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:47.817][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.818][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:47.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:47.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.823][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:47.824][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:47.825][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.825][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.827][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:47.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:47.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.830][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:47.831][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:47.832][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.833][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.834][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:47.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:47.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.853][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.863][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.867][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:47.875][self$createEntryFromContent] Accession numbers: 57310. biodb.TRACE[2024-07-06 16:01:47.876][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.880][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:47.891][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:47.892][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:47.893][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:47.897][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:47.898][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:47.899][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:47.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:47.900][private$loadEntries] Creating entries from ids [1]: "66216". biodb.DEBUG[2024-07-06 16:01:47.901][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:47.903][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216". biodb.TRACE[2024-07-06 16:01:47.904][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:47.905][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml". biodb.DEBUG[2024-07-06 16:01:47.906][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:47.907][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:47.909][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:47.910][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:47.911][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:47.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:47.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:47.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:47.917][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:47.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:47.920][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.921][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.922][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.923][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:47.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:47.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.927][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:47.928][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:47.929][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.930][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.931][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:47.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:47.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.935][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:47.936][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:47.937][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.937][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.938][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:47.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:47.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.942][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:47.943][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:47.944][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.945][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.946][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:47.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:47.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.949][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:47.950][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:47.951][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.952][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.953][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:47.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:47.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.957][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.958][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:47.959][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.959][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.961][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:47.962][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.962][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.963][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.964][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:47.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:47.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.968][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.969][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.970][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.971][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:47.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.975][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:47.976][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:47.977][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.978][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.979][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:47.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:47.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.983][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:47.984][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:47.985][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.986][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.987][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:47.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:47.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.990][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:47.991][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:47.992][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.993][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.994][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:47.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:47.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:47.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:47.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:47.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:48.034][self$createEntryFromContent] Accession numbers: 66216. biodb.TRACE[2024-07-06 16:01:48.035][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.038][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:48.050][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:48.051][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:48.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:48.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:48.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:48.057][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:48.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:48.059][private$loadEntries] Creating entries from ids [1]: "70860". biodb.DEBUG[2024-07-06 16:01:48.060][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:48.061][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860". biodb.TRACE[2024-07-06 16:01:48.062][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:48.064][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml". biodb.DEBUG[2024-07-06 16:01:48.065][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:48.066][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:48.067][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:48.068][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:48.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:48.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:48.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:48.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:48.075][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:48.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:48.078][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.079][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.080][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.081][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.086][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:48.087][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:48.087][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.088][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.089][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:48.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:48.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.093][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:48.094][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:48.095][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.096][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.097][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:48.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:48.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.101][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:48.102][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:48.102][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.103][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.104][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:48.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:48.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.108][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:48.109][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:48.110][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.111][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.112][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:48.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:48.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.115][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:48.116][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:48.117][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.118][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.119][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:48.120][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.121][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.122][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.123][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:48.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.127][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.128][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.128][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.129][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.134][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:48.135][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:48.136][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.137][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.138][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:48.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:48.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.141][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:48.142][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:48.143][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.144][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.145][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:48.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:48.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.149][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:48.150][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:48.151][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.152][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.153][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:48.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:48.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.182][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:48.192][self$createEntryFromContent] Accession numbers: 70860. biodb.TRACE[2024-07-06 16:01:48.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.200][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.203][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:48.208][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:48.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:48.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:48.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:48.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:48.216][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:48.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:48.218][private$loadEntries] Creating entries from ids [1]: "70861". biodb.DEBUG[2024-07-06 16:01:48.219][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:48.220][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861". biodb.TRACE[2024-07-06 16:01:48.221][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:48.223][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml". biodb.DEBUG[2024-07-06 16:01:48.224][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:48.225][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:48.226][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:48.227][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:48.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:48.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:48.233][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:48.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:48.235][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:48.235][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:48.237][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.238][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.239][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.240][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.245][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:48.246][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:48.247][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.247][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.249][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:48.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:48.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.252][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:48.253][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:48.254][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.255][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.256][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:48.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:48.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.260][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:48.261][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:48.261][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.262][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.263][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:48.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:48.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.267][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:48.268][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:48.269][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.270][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:48.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:48.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.275][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:48.275][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:48.276][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.277][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.278][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:48.279][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.280][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.281][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.282][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:48.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.286][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.287][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.288][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.288][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.289][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.293][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:48.294][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:48.295][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.296][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.297][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:48.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:48.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.301][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:48.302][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:48.302][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.303][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.304][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:48.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:48.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.308][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:48.309][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:48.310][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.311][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.312][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:48.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:48.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.340][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.343][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.348][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:48.351][self$createEntryFromContent] Accession numbers: 70861. biodb.TRACE[2024-07-06 16:01:48.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:48.363][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:48.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:48.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:48.373][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:48.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:48.375][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:48.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:48.377][private$loadEntries] Creating entries from ids [1]: "78662". biodb.DEBUG[2024-07-06 16:01:48.378][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:48.379][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662". biodb.TRACE[2024-07-06 16:01:48.380][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:48.381][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml". biodb.DEBUG[2024-07-06 16:01:48.382][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:48.384][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:48.385][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:48.386][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:48.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:48.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:48.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:48.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:48.393][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:48.394][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:48.396][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.397][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.398][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.399][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.404][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:48.405][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:48.405][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.406][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.407][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:48.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:48.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.411][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:48.412][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:48.413][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.414][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.415][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:48.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:48.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.419][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:48.419][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:48.420][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.421][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.422][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:48.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:48.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.426][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:48.427][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:48.428][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.429][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.430][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:48.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:48.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.432][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.433][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:48.434][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:48.435][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.436][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.437][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:48.438][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.439][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.440][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.441][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:48.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.445][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.446][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.446][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.447][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.452][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:48.453][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:48.454][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.455][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.456][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:48.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:48.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.460][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:48.461][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:48.462][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.462][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.464][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:48.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:48.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.466][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.467][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:48.468][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:48.469][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.470][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.471][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:48.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:48.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.475][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.477][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.481][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.488][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.489][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.506][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:48.511][self$createEntryFromContent] Accession numbers: 78662. biodb.TRACE[2024-07-06 16:01:48.512][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.519][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:48.523][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:48.523][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:48.524][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:48.528][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:48.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:48.534][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:48.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:48.536][private$loadEntries] Creating entries from ids [1]: "85084". biodb.DEBUG[2024-07-06 16:01:48.537][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:48.539][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084". biodb.TRACE[2024-07-06 16:01:48.540][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:48.541][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml". biodb.DEBUG[2024-07-06 16:01:48.542][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:48.543][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:48.544][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:48.546][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:48.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:48.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:48.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:48.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:48.553][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:48.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:48.556][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.557][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.558][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.559][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.563][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:48.564][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:48.565][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.566][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.567][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:48.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:48.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.571][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:48.572][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:48.573][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.574][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.575][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:48.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:48.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.578][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:48.579][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:48.580][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.581][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.582][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:48.583][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:48.584][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.585][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.586][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:48.587][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:48.588][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.588][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.590][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:48.591][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.591][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.592][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.593][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:48.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.596][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.597][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.598][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.599][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.600][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.604][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:48.605][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:48.606][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.607][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.608][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:48.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:48.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.611][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.612][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:48.613][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:48.614][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.615][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.616][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:48.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:48.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.619][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:48.620][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:48.621][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.622][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.626][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.637][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.638][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.655][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.659][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:48.660][self$createEntryFromContent] Accession numbers: 85084. biodb.TRACE[2024-07-06 16:01:48.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.663][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.671][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:48.671][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:48.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:48.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:48.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:48.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:48.679][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:48.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:48.681][private$loadEntries] Creating entries from ids [1]: "85086". biodb.DEBUG[2024-07-06 16:01:48.682][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:48.683][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086". biodb.TRACE[2024-07-06 16:01:48.684][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:48.686][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml". biodb.DEBUG[2024-07-06 16:01:48.687][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:48.688][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:48.689][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:48.690][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:48.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:48.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:48.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:48.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:48.702][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:48.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:48.705][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.706][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.707][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.708][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.713][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:48.714][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:48.714][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.715][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.717][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:48.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:48.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.720][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:48.721][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:48.722][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.723][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.724][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:48.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:48.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.728][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:48.729][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:48.729][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.730][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.731][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:48.732][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:48.733][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.734][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.735][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:48.736][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:48.737][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.738][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.739][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:48.740][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.741][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.742][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.743][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:48.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.746][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.747][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.748][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.749][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.750][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.754][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:48.755][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:48.756][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.757][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.758][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:48.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:48.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.761][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:48.762][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:48.763][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.764][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.765][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:48.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:48.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.769][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:48.770][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:48.771][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.772][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.776][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.784][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:48.809][self$createEntryFromContent] Accession numbers: 85086. biodb.TRACE[2024-07-06 16:01:48.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.820][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:48.821][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:48.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:48.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:48.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:48.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:48.829][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:48.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:48.830][private$loadEntries] Creating entries from ids [1]: "88123". biodb.DEBUG[2024-07-06 16:01:48.831][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:48.833][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123". biodb.TRACE[2024-07-06 16:01:48.834][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:48.835][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml". biodb.DEBUG[2024-07-06 16:01:48.836][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:48.838][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:48.839][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:48.840][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:48.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:48.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:48.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:48.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:48.847][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:48.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:48.850][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.851][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.852][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.853][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.863][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:48.864][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:48.865][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.866][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.867][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:48.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:48.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.870][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:48.871][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:48.872][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.873][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.874][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:48.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:48.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.878][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:48.879][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:48.880][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.881][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.882][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:48.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:48.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.886][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:48.887][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:48.887][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.888][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.889][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:48.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:48.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.893][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:48.894][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:48.895][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.896][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.897][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:48.898][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.899][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.900][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.901][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:48.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.905][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.905][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.906][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.907][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:48.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.912][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:48.913][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:48.914][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.915][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.916][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:48.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:48.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.920][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:48.921][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:48.922][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.922][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.924][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:48.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:48.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.927][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:48.928][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:48.929][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.930][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.931][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:48.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:48.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:48.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.963][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:48.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:48.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:48.971][self$createEntryFromContent] Accession numbers: 88123. biodb.TRACE[2024-07-06 16:01:48.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:48.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:48.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:48.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:48.988][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:48.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:48.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:48.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:48.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:48.998][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:48.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:49.000][private$loadEntries] Creating entries from ids [1]: "134117". biodb.DEBUG[2024-07-06 16:01:49.001][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:49.003][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117". biodb.TRACE[2024-07-06 16:01:49.004][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:49.006][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml". biodb.DEBUG[2024-07-06 16:01:49.007][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:49.008][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:49.010][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:49.012][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:49.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:49.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:49.018][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:49.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:49.020][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:49.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:49.024][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.025][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.026][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.026][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.032][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:49.047][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:49.049][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.050][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.051][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:49.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:49.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.055][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:49.056][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:49.057][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.058][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.059][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:49.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:49.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.063][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:49.064][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:49.065][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.066][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.067][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:49.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:49.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.071][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:49.072][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:49.073][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.074][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.075][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:49.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:49.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.079][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:49.080][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:49.081][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.082][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.083][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:49.084][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.085][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.086][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.087][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:49.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.091][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.092][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.093][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.094][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.099][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:49.100][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:49.101][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.102][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.103][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:49.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:49.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.107][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:49.108][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:49.109][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.110][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.111][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:49.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:49.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.115][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:49.116][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:49.117][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.118][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.119][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:49.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:49.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.123][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.127][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.134][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.150][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.158][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:49.162][self$createEntryFromContent] Accession numbers: 134117. biodb.TRACE[2024-07-06 16:01:49.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:49.174][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:49.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:49.175][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:49.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:49.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:49.181][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:49.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:49.183][private$loadEntries] Creating entries from ids [1]: "138307". biodb.DEBUG[2024-07-06 16:01:49.184][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:49.185][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307". biodb.TRACE[2024-07-06 16:01:49.186][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:49.188][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml". biodb.DEBUG[2024-07-06 16:01:49.189][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:49.190][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:49.191][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:49.192][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:49.193][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:49.194][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:49.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:49.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:49.200][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:49.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:49.202][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.203][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.204][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.205][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.210][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:49.211][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:49.212][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.213][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.218][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:49.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:49.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.222][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:49.223][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:49.224][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.225][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.226][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:49.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:49.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.229][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:49.230][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:49.231][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.232][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.233][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:49.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:49.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.237][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:49.238][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:49.238][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.239][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.240][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:49.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:49.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.244][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:49.245][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:49.246][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.247][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.248][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:49.249][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.250][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.250][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.252][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:49.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.254][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.255][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.256][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.257][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.258][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.259][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.263][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:49.264][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:49.264][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.265][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.266][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:49.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:49.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.270][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:49.271][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:49.272][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.273][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.274][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:49.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:49.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.277][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:49.278][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:49.279][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.280][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.281][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:49.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:49.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.285][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.303][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.305][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.306][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.309][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.316][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:49.321][self$createEntryFromContent] Accession numbers: 138307. biodb.TRACE[2024-07-06 16:01:49.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:49.333][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:49.333][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:49.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:49.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:49.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:49.340][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:49.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:49.342][private$loadEntries] Creating entries from ids [1]: "176803". biodb.DEBUG[2024-07-06 16:01:49.343][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:49.344][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803". biodb.TRACE[2024-07-06 16:01:49.345][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:49.347][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml". biodb.DEBUG[2024-07-06 16:01:49.348][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:49.349][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:49.350][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:49.351][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:49.352][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:49.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:49.357][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:49.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:49.358][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:49.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:49.362][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.362][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.363][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.364][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.369][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:49.370][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:49.371][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.372][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.373][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:49.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:49.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.381][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:49.382][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:49.383][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.384][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.385][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:49.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:49.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.389][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:49.389][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:49.390][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.391][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.392][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:49.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:49.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.396][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:49.397][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:49.398][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.399][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.400][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:49.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:49.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.403][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:49.404][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:49.405][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.406][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.407][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:49.408][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.409][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.410][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.411][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:49.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.415][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.416][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.416][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.417][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.418][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.421][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.422][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:49.423][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:49.424][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.425][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:49.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:49.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.429][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:49.430][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:49.431][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.432][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.433][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:49.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:49.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.437][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:49.438][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:49.439][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.439][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.441][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:49.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:49.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.448][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.455][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.457][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.458][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.466][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.476][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:49.480][self$createEntryFromContent] Accession numbers: 176803. biodb.TRACE[2024-07-06 16:01:49.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.488][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.491][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:49.492][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:49.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:49.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:49.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:49.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:49.499][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:49.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:49.501][private$loadEntries] Creating entries from ids [1]: "176962". biodb.DEBUG[2024-07-06 16:01:49.502][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:49.503][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962". biodb.TRACE[2024-07-06 16:01:49.504][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:49.506][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml". biodb.DEBUG[2024-07-06 16:01:49.507][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:49.508][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:49.509][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:49.510][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:49.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:49.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:49.516][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:49.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:49.517][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:49.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:49.520][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.521][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.522][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.523][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.524][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.528][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:49.529][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:49.530][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.530][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.531][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:49.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:49.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.540][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:49.541][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:49.542][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.542][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.544][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:49.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:49.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.547][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:49.548][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:49.549][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.550][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.551][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:49.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:49.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.554][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:49.555][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:49.556][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.557][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.558][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:49.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:49.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.561][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.562][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:49.563][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:49.564][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.565][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.566][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:49.567][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.567][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.568][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.569][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:49.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.573][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.574][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.575][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.576][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.580][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:49.581][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:49.582][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.583][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:49.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:49.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.588][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:49.589][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:49.590][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.591][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.592][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:49.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:49.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.595][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:49.596][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:49.597][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.598][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.599][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:49.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:49.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.610][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.620][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.624][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:49.638][self$createEntryFromContent] Accession numbers: 176962. biodb.TRACE[2024-07-06 16:01:49.639][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.642][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.647][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.649][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:49.650][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:49.651][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:49.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:49.656][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:49.657][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:49.658][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:49.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:49.659][private$loadEntries] Creating entries from ids [1]: "198655". biodb.DEBUG[2024-07-06 16:01:49.660][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:49.662][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655". biodb.TRACE[2024-07-06 16:01:49.663][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:49.664][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml". biodb.DEBUG[2024-07-06 16:01:49.665][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:49.666][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:49.667][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:49.669][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:49.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:49.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:49.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:49.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:49.676][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:49.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:49.679][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.680][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.681][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.682][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.686][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:49.687][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:49.688][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.689][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.690][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:49.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:49.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.693][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.694][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:49.699][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:49.700][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.701][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.702][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:49.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:49.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.706][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:49.707][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:49.708][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.709][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.710][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:49.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:49.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.713][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:49.714][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:49.715][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.716][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.717][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:49.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:49.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.721][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:49.722][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:49.723][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.724][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.725][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:49.726][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.727][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.727][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.728][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:49.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.732][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.733][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.734][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.735][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.739][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.740][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:49.741][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:49.741][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.742][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.743][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:49.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:49.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.747][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:49.748][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:49.749][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.750][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.751][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:49.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:49.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.754][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:49.755][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:49.756][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.757][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.758][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:49.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:49.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.765][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.773][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.791][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.793][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:49.798][self$createEntryFromContent] Accession numbers: 198655. biodb.TRACE[2024-07-06 16:01:49.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:49.810][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:49.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:49.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:49.815][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:49.816][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:49.817][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:49.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:49.819][private$loadEntries] Creating entries from ids [1]: "215045". biodb.DEBUG[2024-07-06 16:01:49.820][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:49.821][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045". biodb.TRACE[2024-07-06 16:01:49.822][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:49.824][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml". biodb.DEBUG[2024-07-06 16:01:49.825][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:49.826][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:49.827][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:49.828][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:49.829][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:49.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:49.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:49.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:49.835][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:49.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:49.838][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.839][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.840][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.841][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.846][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:49.847][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:49.847][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.848][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.849][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:49.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:49.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.853][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:49.854][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:49.855][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.860][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.862][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:49.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:49.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.865][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:49.866][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:49.867][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.868][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.869][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:49.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:49.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.873][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:49.874][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:49.875][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.875][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.876][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:49.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:49.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.880][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:49.881][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:49.882][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.883][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.884][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:49.885][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.886][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.887][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.888][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:49.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.891][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.892][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.893][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.894][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:49.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.899][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:49.900][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:49.901][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.901][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.903][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:49.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:49.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.906][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:49.907][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:49.908][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.909][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.910][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:49.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:49.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.914][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:49.915][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:49.915][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.916][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.917][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:49.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:49.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.921][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.924][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.932][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:49.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.945][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:49.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:49.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:49.957][self$createEntryFromContent] Accession numbers: 215045. biodb.TRACE[2024-07-06 16:01:49.958][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.962][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:49.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:49.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:49.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:49.984][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:01:49.987][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:01:49.988][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-07-06 16:01:49.989][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:49.990][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2024-07-06 16:01:49.993][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:49.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:49.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:49.998][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:49.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.000][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.005][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.012][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.013][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.014][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.023][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.024][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.030][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.036][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.044][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.052][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.053][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.057][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.060][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.072][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.079][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.081][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.091][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.099][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.106][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.111][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.112][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.115][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.119][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.124][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.126][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.135][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.139][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.146][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.159][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.160][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.165][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.166][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.183][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.184][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.189][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.190][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.190][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.192][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.195][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.198][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.203][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.204][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.208][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.209][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.210][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.215][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.223][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.223][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.230][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.242][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.249][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.254][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.255][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.262][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.269][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.271][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.274][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.278][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.281][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.282][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.287][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.289][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.290][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.297][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.298][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.301][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.308][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.310][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.314][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.316][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.317][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.321][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.322][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.328][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.338][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.341][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.345][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.350][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.352][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.365][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.366][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.366][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.370][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.372][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.385][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.392][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.394][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.397][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.400][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.405][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.412][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.414][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.416][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.417][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.478][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:01:50.481][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:01:50.482][cch$loadFileContent] Trying to load 1 files from cache: [1]: "c5171beada848a87ef2ffa10427d9be3". biodb.TRACE[2024-07-06 16:01:50.483][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:50.484][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content". biodb.DEBUG[2024-07-06 16:01:50.487][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:01:50.495][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:01:50.496][cch$loadFileContent] Trying to load 1 files from cache: [1]: "750e63ff76a843f016511fa71c89113e". biodb.TRACE[2024-07-06 16:01:50.497][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:50.499][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content". biodb.DEBUG[2024-07-06 16:01:50.501][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.501][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.502][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.506][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.507][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.508][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:50.510][private$loadEntries] Creating entries from ids [1]: "4648". biodb.DEBUG[2024-07-06 16:01:50.511][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:50.512][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648". biodb.TRACE[2024-07-06 16:01:50.513][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:50.515][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml". biodb.DEBUG[2024-07-06 16:01:50.516][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:50.517][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:50.518][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:50.519][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.525][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.526][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.529][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.530][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.531][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.532][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.537][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:50.537][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:50.538][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.539][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.540][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:50.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:50.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.544][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:50.545][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:50.546][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.547][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.548][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:50.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:50.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.552][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:50.553][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:50.553][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.554][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.555][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:50.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:50.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.559][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:50.560][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:50.561][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.562][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.563][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:50.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:50.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.566][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:50.567][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:50.568][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.569][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.570][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:50.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:50.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.574][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:50.575][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.576][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.576][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.577][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:50.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.581][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.582][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.583][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.584][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.589][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:50.590][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:50.591][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.591][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.593][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:50.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:50.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.596][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:50.597][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:50.598][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.599][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.600][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:50.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:50.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.604][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:50.605][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:50.606][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.607][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.608][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:50.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:50.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:50.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:50.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:50.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:50.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.619][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:50.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:50.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.633][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.636][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.648][self$createEntryFromContent] Accession numbers: 4648. biodb.TRACE[2024-07-06 16:01:50.649][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.657][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.661][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.664][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.665][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.666][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.673][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.686][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.693][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:50.695][private$loadEntries] Creating entries from ids [1]: "62447". biodb.DEBUG[2024-07-06 16:01:50.696][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:50.697][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447". biodb.TRACE[2024-07-06 16:01:50.698][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:50.700][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml". biodb.DEBUG[2024-07-06 16:01:50.701][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:50.702][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:50.703][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:50.704][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.712][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.715][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.716][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.717][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.717][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.722][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:50.723][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:50.724][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.725][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.726][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:50.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:50.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.729][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.730][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:50.731][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:50.732][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.733][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.734][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:50.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:50.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.737][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:50.738][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:50.739][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.740][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.741][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:50.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:50.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.745][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:50.746][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:50.747][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.748][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:50.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:50.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.753][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:50.754][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:50.755][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.755][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.757][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:50.757][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.758][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.759][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.760][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:50.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:50.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.764][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.765][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.766][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.767][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.772][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:50.773][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:50.774][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.774][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.776][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:50.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:50.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.780][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:50.781][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:50.781][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.782][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.784][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:50.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:50.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.787][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:50.788][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:50.789][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.790][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.791][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:50.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:50.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.795][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:50.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:50.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:50.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:50.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:50.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:50.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.813][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:50.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:50.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.837][self$createEntryFromContent] Accession numbers: 62447. biodb.TRACE[2024-07-06 16:01:50.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.864][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:01:50.867][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:01:50.868][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-07-06 16:01:50.869][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:50.870][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2024-07-06 16:01:50.873][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.878][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.880][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.893][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.900][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.908][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.920][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.926][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.928][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.948][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.954][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.955][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.956][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.961][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.963][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.968][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.972][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:50.975][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:50.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:50.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:50.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:50.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:50.991][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:50.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:50.992][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:50.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:50.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:50.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.003][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.011][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.023][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.031][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.043][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.051][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.064][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.069][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.070][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.071][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.084][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.086][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.090][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.091][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.091][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.100][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.104][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.111][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.124][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.131][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.149][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.156][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.169][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.170][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.171][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.175][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.177][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.177][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.178][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.186][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.189][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.197][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.209][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.217][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.229][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.230][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.236][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.246][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.249][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.257][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.269][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.270][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.275][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.277][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.290][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.290][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.297][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.311][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.329][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:01:51.332][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:01:51.333][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2". biodb.TRACE[2024-07-06 16:01:51.335][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:51.336][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content". biodb.DEBUG[2024-07-06 16:01:51.339][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.339][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.345][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.347][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.351][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.358][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.365][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.378][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.385][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.386][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.387][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.392][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.401][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.412][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.420][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.432][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.440][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.447][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.455][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.459][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.460][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.461][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.472][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.477][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.478][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.481][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.485][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.493][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.498][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.505][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.506][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.511][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.513][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.513][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.518][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.522][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.525][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.526][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.532][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.545][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.552][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.554][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.558][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.564][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.565][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.572][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.581][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.585][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.585][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.592][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.594][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.596][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.597][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.601][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.605][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.605][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.612][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.613][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.624][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.637][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.645][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.649][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.650][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.650][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.651][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.657][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.661][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.662][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.669][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.675][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.676][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.677][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.679][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.689][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.690][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.695][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.696][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.696][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.702][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.709][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.715][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.716][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.729][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.730][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.734][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.736][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.745][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.748][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.749][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.750][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.750][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.754][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.755][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.756][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:51.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.780][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-07-06 16:01:51.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-07-06 16:01:51.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-07-06 16:01:51.794][biodb::testThat] biodb.INFO [2024-07-06 16:01:51.795][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. "). biodb.INFO [2024-07-06 16:01:51.796][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-07-06 16:01:51.797][biodb::testThat] biodb.TRACE[2024-07-06 16:01:51.800][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-07-06 16:01:51.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-07-06 16:01:51.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.803][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-07-06 16:01:51.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-07-06 16:01:51.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.806][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.807][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-07-06 16:01:51.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-07-06 16:01:51.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.814][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.822][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.825][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.829][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.836][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.843][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.857][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.858][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.859][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.863][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.864][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.865][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:51.868][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:01:51.871][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:01:51.872][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-07-06 16:01:51.873][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:51.875][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-07-06 16:01:51.877][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.882][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.884][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.886][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.893][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.896][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.897][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:01:51.900][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:01:51.901][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-07-06 16:01:51.903][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:01:51.904][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-07-06 16:01:51.906][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.913][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.926][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.932][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.933][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.934][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.936][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.939][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:51.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:51.947][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:01:51.948][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:51.949][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:51.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:51.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:51.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:51.960][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:51.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:51.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:51.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:51.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:51.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:51.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.969][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:51.970][private$selectFields] biodb.TRACE[2024-07-06 16:01:51.971][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:01:51.972][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:01:51.973][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:51.974][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:51.975][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:51.975][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.976][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.977][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:51.978][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:51.979][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.980][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.981][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:51.982][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:51.983][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:51.983][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:51.984][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.985][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.986][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:01:51.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:51.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:51.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:51.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:51.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:51.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:51.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:51.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:51.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:52.006][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288]. biodb.DEBUG[2024-07-06 16:01:52.007][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:52.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:52.009][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:52.013][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:52.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:52.015][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:52.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:52.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:52.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:52.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:52.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:52.024][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:52.025][private$selectFields] biodb.TRACE[2024-07-06 16:01:52.025][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:01:52.026][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:01:52.027][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:52.028][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.029][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.030][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:52.031][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:52.032][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.033][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.033][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:52.034][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:52.035][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:52.036][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:52.037][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.038][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.039][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:52.040][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:52.040][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:01:52.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:52.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:52.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:52.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:52.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:52.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:52.052][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-07-06 16:01:52.053][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:52.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:52.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:52.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:52.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:52.061][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:52.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:52.063][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:52.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:52.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:52.069][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:52.070][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:52.071][private$selectFields] biodb.TRACE[2024-07-06 16:01:52.072][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:01:52.072][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:01:52.073][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:52.074][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.075][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.076][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:52.077][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:52.078][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.079][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.080][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:52.080][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:52.081][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:52.082][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:52.083][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.084][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.085][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:52.086][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:52.087][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:01:52.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:52.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:52.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:52.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:52.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:52.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:52.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:52.099][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892]. biodb.DEBUG[2024-07-06 16:01:52.100][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:01:52.100][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:01:52.104][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:52.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:52.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:52.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:52.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:52.116][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:52.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:52.119][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:01:52.122][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:01:52.123][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:01:52.124][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:01:52.518][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:01:52.959][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:01:52.964][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b3cd8ddf08f509014f10dc9bf7c1649d.content" biodb.TRACE[2024-07-06 16:01:52.996][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b3cd8ddf08f509014f10dc9bf7c1649d.request" biodb.DEBUG[2024-07-06 16:01:53.001][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:53.002][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:53.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:53.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:53.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:53.013][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:53.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:53.016][private$loadEntries] Creating entries from ids [1]: "113227". biodb.DEBUG[2024-07-06 16:01:53.017][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:53.019][cch$loadFileContent] Trying to load 1 files from cache: [1]: "113227". biodb.TRACE[2024-07-06 16:01:53.021][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:01:53.022][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:01:53.024][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:53.025][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:01:53.026][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:01:53.027][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:01:53.030][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:53.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:53.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:53.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:53.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:53.045][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:53.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:53.048][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=113227". biodb.DEBUG[2024-07-06 16:01:53.065][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:01:53.066][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:01:53.082][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=113227". biodb.TRACE[2024-07-06 16:01:53.476][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=113227). biodb.DEBUG[2024-07-06 16:01:53.915][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:01:53.920][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ed496dac459a2ba62e671edbcae22326.content" biodb.TRACE[2024-07-06 16:01:53.928][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ed496dac459a2ba62e671edbcae22326.request" biodb.TRACE[2024-07-06 16:01:53.934][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/113227.xml" biodb.DEBUG[2024-07-06 16:01:53.937][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:01:53.940][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:53.943][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:53.947][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:53.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:53.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:53.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:53.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:53.965][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:53.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:53.971][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:53.973][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:53.975][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:53.976][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:53.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:53.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:53.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:53.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:53.984][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:53.986][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:53.987][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:53.988][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:53.990][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:53.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:53.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:53.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:53.995][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:53.996][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:53.997][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:53.998][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.000][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:54.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:54.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.004][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:54.005][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:54.006][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.007][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.008][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:54.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:54.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.031][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:54.032][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:54.034][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.035][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.036][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:54.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:54.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.040][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:54.041][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:54.042][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.043][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.044][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:54.045][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:54.046][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.047][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.048][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:54.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:54.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.052][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:54.053][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:54.054][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.055][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:54.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:54.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.060][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:54.061][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:54.062][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.063][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:54.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:54.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.068][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:54.069][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:54.070][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.071][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.072][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:54.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:54.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.076][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:54.077][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:54.078][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.079][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.080][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:54.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:54.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:54.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:54.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:54.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:54.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:54.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:54.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:54.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:54.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.098][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:54.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:54.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.101][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.102][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:54.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:54.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:54.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:54.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:54.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:54.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:54.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:54.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:54.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:54.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:54.120][self$createEntryFromContent] Accession numbers: 113227. biodb.TRACE[2024-07-06 16:01:54.121][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:54.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:54.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:54.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:54.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:54.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:54.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:54.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:54.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:54.132][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:54.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:54.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:54.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:54.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:54.139][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:54.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:54.141][private$loadEntries] Creating entries from ids [1]: "169712". biodb.DEBUG[2024-07-06 16:01:54.142][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:54.143][cch$loadFileContent] Trying to load 1 files from cache: [1]: "169712". biodb.TRACE[2024-07-06 16:01:54.144][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:01:54.145][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:01:54.146][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:54.147][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:01:54.148][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:01:54.149][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:01:54.162][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:54.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:54.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:54.168][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:54.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:54.169][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:54.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:54.171][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169712". biodb.DEBUG[2024-07-06 16:01:54.173][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:01:54.174][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:01:54.175][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169712". biodb.TRACE[2024-07-06 16:01:54.576][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169712). biodb.DEBUG[2024-07-06 16:01:55.005][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:01:55.010][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6e52d7b9d801aec68d97cc03bd4acc90.content" biodb.TRACE[2024-07-06 16:01:55.017][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6e52d7b9d801aec68d97cc03bd4acc90.request" biodb.TRACE[2024-07-06 16:01:55.035][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/169712.xml" biodb.DEBUG[2024-07-06 16:01:55.039][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:01:55.042][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:55.044][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:55.047][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:55.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:55.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:55.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:55.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:55.061][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:55.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:55.066][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:55.068][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:55.069][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.070][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:55.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:55.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.077][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:55.078][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:55.080][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.081][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.082][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:55.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:55.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.087][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:55.088][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:55.089][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.090][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.091][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:55.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:55.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.095][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:55.096][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:55.097][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.098][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.099][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:55.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:55.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.103][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:55.104][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:55.105][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.106][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.107][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:55.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:55.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.111][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:55.112][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:55.113][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.113][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.115][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:55.116][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:55.116][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.117][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.118][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:55.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:55.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.122][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:55.123][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:55.124][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.125][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:55.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:55.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.130][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:55.130][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:55.131][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.132][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.133][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:55.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:55.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.137][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:55.138][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:55.139][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.140][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.141][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:55.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:55.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.145][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:55.146][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:55.146][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.147][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.148][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:55.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:55.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:55.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:55.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:55.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:55.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:55.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:55.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:55.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:55.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:55.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:55.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:55.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:55.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:55.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:55.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:55.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:55.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:55.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:55.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:55.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:55.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:55.188][self$createEntryFromContent] Accession numbers: 169712. biodb.TRACE[2024-07-06 16:01:55.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:55.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:55.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:55.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:55.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:55.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:55.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:55.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:55.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:55.201][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:01:55.204][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:01:55.205][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:01:55.206][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:01:55.604][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:01:56.050][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:01:56.055][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/831507e33c6cf42061851262412f5feb.content" biodb.TRACE[2024-07-06 16:01:56.063][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/831507e33c6cf42061851262412f5feb.request" biodb.DEBUG[2024-07-06 16:01:56.069][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:56.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:56.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:56.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:56.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:56.089][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:56.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:56.094][private$loadEntries] Creating entries from ids [1]: "4781". biodb.DEBUG[2024-07-06 16:01:56.096][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:56.099][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4781". biodb.TRACE[2024-07-06 16:01:56.102][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:01:56.104][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:01:56.107][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:56.109][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:01:56.111][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:01:56.112][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:01:56.117][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:56.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:56.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:56.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:56.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:56.129][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:56.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:56.131][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4781". biodb.DEBUG[2024-07-06 16:01:56.135][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:01:56.136][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:01:56.138][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4781". biodb.TRACE[2024-07-06 16:01:56.535][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4781). biodb.DEBUG[2024-07-06 16:01:57.077][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:01:57.082][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e4869054c906476bc1e4ece10c7e53cc.content" biodb.TRACE[2024-07-06 16:01:57.089][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e4869054c906476bc1e4ece10c7e53cc.request" biodb.TRACE[2024-07-06 16:01:57.094][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4781.xml" biodb.DEBUG[2024-07-06 16:01:57.097][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:01:57.100][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:57.102][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:57.106][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:57.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:57.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:57.119][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:57.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:57.122][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:57.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:57.128][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:57.130][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:57.131][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.133][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:57.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:57.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.141][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:57.142][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:57.143][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.145][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.146][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:57.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:57.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.151][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:57.153][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:57.154][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.155][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.157][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:57.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:57.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.161][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:57.162][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:57.163][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.164][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.166][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:57.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:57.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.170][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:57.171][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:57.171][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.172][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.174][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:57.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:57.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.177][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:57.178][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:57.179][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.180][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.182][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:57.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:57.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.185][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:57.186][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:57.187][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.188][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.189][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:57.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:57.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.193][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:57.194][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:57.195][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.196][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:57.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:57.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.200][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.201][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:57.202][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:57.202][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.203][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.205][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:57.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:57.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.208][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:57.209][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:57.210][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.211][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.212][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:57.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:57.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.216][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:57.217][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:57.218][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.219][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.220][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:57.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:57.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:57.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:57.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:57.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:57.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:57.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:57.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.242][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:57.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:57.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:57.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:57.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:57.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:57.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:57.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:57.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:57.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:57.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:57.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:57.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:57.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:57.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:57.268][self$createEntryFromContent] Accession numbers: 4781. biodb.TRACE[2024-07-06 16:01:57.269][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:57.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:57.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:57.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:57.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:57.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:57.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:57.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:57.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:57.280][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:57.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:57.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:57.286][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:57.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:57.287][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:57.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:57.289][private$loadEntries] Creating entries from ids [1]: "16587". biodb.DEBUG[2024-07-06 16:01:57.290][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:57.292][cch$loadFileContent] Trying to load 1 files from cache: [1]: "16587". biodb.TRACE[2024-07-06 16:01:57.293][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:01:57.294][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:01:57.295][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:57.296][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:01:57.297][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:01:57.297][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:01:57.300][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:57.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:57.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:57.306][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:57.307][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:57.307][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:57.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:57.309][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=16587". biodb.DEBUG[2024-07-06 16:01:57.312][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:01:57.313][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:01:57.314][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=16587". biodb.TRACE[2024-07-06 16:01:57.723][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=16587). biodb.DEBUG[2024-07-06 16:01:58.159][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:01:58.164][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6012905c0932919c069ecb5afc0b487b.content" biodb.TRACE[2024-07-06 16:01:58.171][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6012905c0932919c069ecb5afc0b487b.request" biodb.TRACE[2024-07-06 16:01:58.176][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/16587.xml" biodb.DEBUG[2024-07-06 16:01:58.179][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:01:58.181][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:58.184][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:58.187][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:58.189][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:58.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:58.200][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:58.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:58.204][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:58.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:58.209][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:58.211][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:58.213][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.214][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:58.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:58.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.222][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:58.224][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:58.225][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.226][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.228][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:58.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:58.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.233][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:58.234][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:58.235][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.236][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.238][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:58.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:58.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.242][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:58.244][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:58.245][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.245][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.247][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:58.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:58.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.251][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:58.252][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:58.253][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.253][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.255][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:58.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:58.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.258][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:58.259][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:58.260][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.261][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.262][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:58.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:58.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.266][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:58.267][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:58.268][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.268][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.270][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:58.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:58.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.281][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:58.282][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:58.283][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.284][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:58.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:58.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.289][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:58.290][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:58.291][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.291][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.293][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:58.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:58.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.296][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:58.297][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:58.298][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.299][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.300][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:58.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:58.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.304][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:58.305][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:58.306][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.307][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.308][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:58.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:58.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:58.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:58.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:58.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:58.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:58.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:58.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:58.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:58.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:58.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:58.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:58.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:58.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:58.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:58.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:58.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:58.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.340][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.341][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:58.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:58.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.343][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:58.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:58.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:58.348][self$createEntryFromContent] Accession numbers: 16587. biodb.TRACE[2024-07-06 16:01:58.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:58.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:58.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:58.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:58.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:58.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:58.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:58.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:58.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:58.359][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:58.360][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:58.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:58.365][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:58.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:58.367][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:58.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:58.369][private$loadEntries] Creating entries from ids [1]: "19804". biodb.DEBUG[2024-07-06 16:01:58.370][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:01:58.371][cch$loadFileContent] Trying to load 1 files from cache: [1]: "19804". biodb.TRACE[2024-07-06 16:01:58.372][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:01:58.373][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:01:58.374][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:01:58.375][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:01:58.376][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:01:58.377][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:01:58.380][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:58.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:58.381][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:58.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:58.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:58.387][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:58.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:58.389][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=19804". biodb.DEBUG[2024-07-06 16:01:58.392][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:01:58.392][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:01:58.394][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=19804". biodb.TRACE[2024-07-06 16:01:58.792][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=19804). biodb.DEBUG[2024-07-06 16:01:59.233][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:01:59.237][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ef7e014212775cbaa9299e60f32b2bcd.content" biodb.TRACE[2024-07-06 16:01:59.244][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ef7e014212775cbaa9299e60f32b2bcd.request" biodb.TRACE[2024-07-06 16:01:59.249][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/19804.xml" biodb.DEBUG[2024-07-06 16:01:59.252][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:01:59.255][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:01:59.257][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:01:59.260][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:59.262][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:59.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:59.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:59.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:59.277][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:59.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:59.282][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:59.284][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:59.286][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.287][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:59.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:59.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.295][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:59.297][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:59.298][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.299][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.301][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:01:59.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:01:59.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.305][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.314][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:59.316][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:59.317][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.318][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.319][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:01:59.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:01:59.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.323][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:59.324][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:59.325][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.326][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.327][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:01:59.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:01:59.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.331][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:59.332][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:59.333][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.334][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.335][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:01:59.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:01:59.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.339][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:59.340][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:01:59.341][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.341][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.343][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:59.344][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:59.344][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.345][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.346][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:01:59.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:59.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.350][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:59.351][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:59.352][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.353][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:59.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:01:59.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.358][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:59.359][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:59.360][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.360][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.362][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:01:59.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:01:59.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.365][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:59.366][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:59.367][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.368][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.369][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:01:59.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:01:59.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.373][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:59.374][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:59.375][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.376][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.377][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:01:59.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:01:59.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.384][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:59.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:59.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:59.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:59.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.399][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:59.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:59.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.401][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:59.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:59.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.406][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:59.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:59.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.409][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:59.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:59.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.412][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:01:59.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:01:59.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.416][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:59.417][self$createEntryFromContent] Accession numbers: 19804. biodb.TRACE[2024-07-06 16:01:59.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:59.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:59.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.421][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:59.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:59.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.425][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:01:59.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:01:59.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:01:59.452][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:01:59.480][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:59.481][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:59.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:59.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:59.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:59.488][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:59.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:59.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.497][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:59.498][private$selectFields] biodb.TRACE[2024-07-06 16:01:59.498][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:01:59.499][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:01:59.500][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:59.501][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.502][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.503][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.504][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.505][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.506][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.506][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.507][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.508][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:59.509][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:59.510][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.511][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.512][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.513][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.513][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:01:59.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.526][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-07-06 16:01:59.527][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:59.527][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:59.528][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:59.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:59.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:59.534][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:59.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:59.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.539][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.543][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:59.544][private$selectFields] biodb.TRACE[2024-07-06 16:01:59.545][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:01:59.545][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:01:59.546][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:59.547][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.548][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.549][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.550][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.551][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.552][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.553][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.553][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.554][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:59.555][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:59.556][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.557][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.558][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.559][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.560][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:01:59.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.572][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-07-06 16:01:59.573][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:59.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:59.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:59.578][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:59.579][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:59.580][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:59.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:01:59.582][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.589][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:59.590][private$selectFields] biodb.TRACE[2024-07-06 16:01:59.591][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:01:59.592][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:01:59.593][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:59.593][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.594][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.595][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.596][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.597][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.598][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.599][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.600][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.601][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:59.601][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:01:59.602][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.603][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.604][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.605][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.606][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:01:59.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:01:59.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:01:59.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:01:59.623][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [19804]. biodb.DEBUG[2024-07-06 16:01:59.624][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:01:59.625][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:01:59.627][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:01:59.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:01:59.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:01:59.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:01:59.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:01:59.634][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:01:59.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:01:59.637][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:01:59.640][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:01:59.641][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:01:59.643][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:02:00.031][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:02:00.455][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:00.460][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26d0872875c47c33e8205aa7124e0486.content" biodb.TRACE[2024-07-06 16:02:00.468][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26d0872875c47c33e8205aa7124e0486.request" biodb.DEBUG[2024-07-06 16:02:00.474][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:00.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:00.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:00.487][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:00.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:00.491][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:00.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:00.495][private$loadEntries] Creating entries from ids [1]: "159630". biodb.DEBUG[2024-07-06 16:02:00.497][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:00.500][cch$loadFileContent] Trying to load 1 files from cache: [1]: "159630". biodb.TRACE[2024-07-06 16:02:00.503][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:00.505][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:00.506][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:00.508][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:00.510][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:00.511][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:00.515][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:00.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:00.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:00.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:00.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:00.526][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:00.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:00.528][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=159630". biodb.DEBUG[2024-07-06 16:02:00.531][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:00.533][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:00.534][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=159630". biodb.TRACE[2024-07-06 16:02:00.938][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=159630). biodb.DEBUG[2024-07-06 16:02:01.381][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:01.385][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f9497c6792bdb2528746e6a81b02589e.content" biodb.TRACE[2024-07-06 16:02:01.392][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f9497c6792bdb2528746e6a81b02589e.request" biodb.TRACE[2024-07-06 16:02:01.397][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/159630.xml" biodb.DEBUG[2024-07-06 16:02:01.400][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:01.403][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:01.405][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:01.409][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:01.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:01.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:01.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:01.424][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:01.425][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:01.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:01.431][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:01.433][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:01.434][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.436][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:01.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:01.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.443][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:01.445][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:01.446][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.447][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.449][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:01.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:01.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.454][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:01.455][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:01.456][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.458][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.459][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:01.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:01.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.462][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.464][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:01.465][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:01.466][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.467][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.468][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:01.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:01.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.472][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:01.473][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:01.474][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.475][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:01.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:01.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.479][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:01.480][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:01.481][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.482][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.483][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:01.484][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:01.485][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.486][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.487][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:01.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:01.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.491][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:01.492][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:01.492][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.493][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:01.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:01.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.498][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:01.499][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:01.500][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.505][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.512][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:01.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:01.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.516][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:01.517][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:01.518][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.519][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.520][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:01.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:01.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.523][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:01.524][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:01.525][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.526][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.527][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:01.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:01.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:01.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:01.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.534][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:01.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:01.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:01.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:01.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.542][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:01.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:01.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:01.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:01.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:01.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:01.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.552][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:01.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:01.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.556][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:01.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:01.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:01.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:01.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:01.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:01.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:01.567][self$createEntryFromContent] Accession numbers: 159630. biodb.TRACE[2024-07-06 16:02:01.568][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:01.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:01.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.572][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:01.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:01.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:01.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:01.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:01.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:01.578][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:01.579][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:01.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:01.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:01.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:01.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:01.586][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:01.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:01.588][private$loadEntries] Creating entries from ids [1]: "160202". biodb.DEBUG[2024-07-06 16:02:01.589][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:01.590][cch$loadFileContent] Trying to load 1 files from cache: [1]: "160202". biodb.TRACE[2024-07-06 16:02:01.591][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:01.592][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:01.593][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:01.594][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:01.595][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:01.596][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:01.599][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:01.599][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:01.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:01.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:01.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:01.606][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:01.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:01.608][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160202". biodb.DEBUG[2024-07-06 16:02:01.610][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:01.611][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:01.613][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160202". biodb.TRACE[2024-07-06 16:02:02.003][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160202). biodb.DEBUG[2024-07-06 16:02:02.435][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:02.440][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1de9586ccaafdf8e637928dc3e313d63.content" biodb.TRACE[2024-07-06 16:02:02.447][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1de9586ccaafdf8e637928dc3e313d63.request" biodb.TRACE[2024-07-06 16:02:02.452][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/160202.xml" biodb.DEBUG[2024-07-06 16:02:02.455][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:02.457][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:02.460][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:02.463][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:02.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:02.467][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:02.476][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:02.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:02.480][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:02.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:02.485][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:02.487][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:02.489][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.490][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:02.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:02.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.498][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:02.500][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:02.501][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.502][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.504][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:02.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:02.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.509][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:02.510][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:02.511][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.512][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.514][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:02.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:02.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.518][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:02.519][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:02.520][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.529][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.530][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:02.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:02.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.534][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:02.535][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:02.536][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.537][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:02.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:02.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.542][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:02.543][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:02.544][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.545][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.546][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:02.547][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:02.548][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.548][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.550][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:02.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:02.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.553][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:02.554][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:02.555][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.556][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:02.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:02.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.561][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:02.562][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:02.563][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.563][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.565][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:02.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:02.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.568][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:02.569][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:02.570][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.571][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.572][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:02.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:02.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.576][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:02.577][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:02.578][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.579][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.580][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:02.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:02.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.582][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:02.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:02.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.586][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:02.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:02.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:02.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:02.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:02.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:02.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:02.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:02.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:02.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:02.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.605][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:02.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:02.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.609][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:02.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:02.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.611][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:02.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:02.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:02.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:02.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:02.620][self$createEntryFromContent] Accession numbers: 160202. biodb.TRACE[2024-07-06 16:02:02.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:02.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:02.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:02.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:02.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:02.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:02.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:02.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:02.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:02.631][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:02.632][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:02.633][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:02.637][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:02.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:02.639][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:02.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:02.641][private$loadEntries] Creating entries from ids [1]: "160393". biodb.DEBUG[2024-07-06 16:02:02.642][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:02.643][cch$loadFileContent] Trying to load 1 files from cache: [1]: "160393". biodb.TRACE[2024-07-06 16:02:02.644][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:02.645][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:02.646][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:02.647][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:02.648][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:02.649][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:02.651][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:02.652][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:02.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:02.657][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:02.658][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:02.659][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:02.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:02.661][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160393". biodb.DEBUG[2024-07-06 16:02:02.663][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:02.664][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:02.665][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160393". biodb.TRACE[2024-07-06 16:02:03.063][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160393). biodb.DEBUG[2024-07-06 16:02:03.494][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:03.498][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e0266c32050b31cda3d5e01c2d907fcd.content" biodb.TRACE[2024-07-06 16:02:03.503][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e0266c32050b31cda3d5e01c2d907fcd.request" biodb.TRACE[2024-07-06 16:02:03.507][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/160393.xml" biodb.DEBUG[2024-07-06 16:02:03.509][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:03.511][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:03.513][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:03.516][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:03.524][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:03.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:03.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:03.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:03.541][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:03.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:03.545][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:03.547][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:03.548][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.549][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:03.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:03.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.556][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:03.557][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:03.558][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.560][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.561][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:03.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:03.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.564][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.566][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:03.567][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:03.568][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.569][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.570][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:03.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:03.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.574][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:03.575][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:03.576][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.577][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.578][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:03.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:03.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.582][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:03.583][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:03.584][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.584][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.586][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:03.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:03.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.589][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:03.590][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:03.591][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.592][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.593][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:03.594][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:03.595][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.596][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.597][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:03.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:03.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.600][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:03.601][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:03.602][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.603][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.604][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:03.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:03.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.608][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:03.609][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:03.610][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.610][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.612][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:03.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:03.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.615][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:03.616][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:03.617][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.618][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.619][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:03.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:03.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.623][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:03.624][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:03.625][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.625][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.626][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:03.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:03.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:03.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:03.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:03.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:03.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.636][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.637][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:03.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:03.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:03.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:03.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:03.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:03.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:03.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:03.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:03.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:03.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.655][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:03.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:03.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:03.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:03.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.663][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:03.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:03.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:03.666][self$createEntryFromContent] Accession numbers: 160393. biodb.TRACE[2024-07-06 16:02:03.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:03.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:03.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:03.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:03.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:03.674][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:03.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:03.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:03.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:03.678][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:03.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:03.680][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:03.684][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:03.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:03.685][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:03.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:03.687][private$loadEntries] Creating entries from ids [1]: "160991". biodb.DEBUG[2024-07-06 16:02:03.688][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:03.689][cch$loadFileContent] Trying to load 1 files from cache: [1]: "160991". biodb.TRACE[2024-07-06 16:02:03.691][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:03.692][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:03.697][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:03.698][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:03.699][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:03.700][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:03.703][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:03.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:03.704][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:03.708][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:03.709][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:03.710][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:03.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:03.712][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160991". biodb.DEBUG[2024-07-06 16:02:03.714][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:03.715][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:03.717][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160991". biodb.TRACE[2024-07-06 16:02:04.113][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=160991). biodb.DEBUG[2024-07-06 16:02:04.549][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:04.554][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6bad8d3e957240d90a71edc1329f8f37.content" biodb.TRACE[2024-07-06 16:02:04.560][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6bad8d3e957240d90a71edc1329f8f37.request" biodb.TRACE[2024-07-06 16:02:04.566][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/160991.xml" biodb.DEBUG[2024-07-06 16:02:04.569][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:04.571][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:04.574][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:04.577][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:04.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:04.581][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:04.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:04.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:04.594][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:04.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:04.599][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:04.601][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:04.603][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.604][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:04.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:04.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.612][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:04.613][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:04.615][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.616][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.618][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:04.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:04.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.623][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:04.624][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:04.625][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.626][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.628][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:04.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:04.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.632][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:04.633][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:04.634][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.635][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.637][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:04.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:04.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.639][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.641][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:04.642][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:04.642][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.643][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.645][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:04.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:04.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.648][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:04.649][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:04.650][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.651][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.652][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:04.653][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:04.654][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.655][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.656][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:04.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:04.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.659][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.660][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:04.661][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:04.661][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.662][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:04.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:04.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.667][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:04.668][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:04.669][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.670][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:04.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:04.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.674][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.675][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:04.676][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:04.677][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.677][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.678][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:04.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:04.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.682][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:04.683][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:04.684][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.685][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.686][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:04.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:04.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:04.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:04.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.692][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:04.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:04.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:04.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:04.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:04.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:04.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:04.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:04.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:04.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:04.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:04.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:04.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.715][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:04.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:04.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:04.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:04.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.729][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:04.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:04.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:04.734][self$createEntryFromContent] Accession numbers: 160991. biodb.TRACE[2024-07-06 16:02:04.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:04.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:04.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:04.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:04.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:04.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:04.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:04.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:04.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:04.746][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:04.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:04.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:04.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:04.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:04.753][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:04.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:04.755][private$loadEntries] Creating entries from ids [1]: "164975". biodb.DEBUG[2024-07-06 16:02:04.756][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:04.757][cch$loadFileContent] Trying to load 1 files from cache: [1]: "164975". biodb.TRACE[2024-07-06 16:02:04.758][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:04.759][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:04.760][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:04.761][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:04.762][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:04.763][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:04.766][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:04.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:04.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:04.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:04.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:04.773][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:04.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:04.775][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=164975". biodb.DEBUG[2024-07-06 16:02:04.778][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:04.778][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:04.780][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=164975". biodb.TRACE[2024-07-06 16:02:05.172][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=164975). biodb.DEBUG[2024-07-06 16:02:05.607][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:05.614][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b1cbfaf7aef2d62dc8db3306c1521943.content" biodb.TRACE[2024-07-06 16:02:05.623][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b1cbfaf7aef2d62dc8db3306c1521943.request" biodb.TRACE[2024-07-06 16:02:05.629][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/164975.xml" biodb.DEBUG[2024-07-06 16:02:05.632][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:05.635][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:05.638][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:05.643][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:05.645][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:05.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:05.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:05.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:05.661][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:05.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:05.668][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:05.670][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:05.671][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.672][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:05.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:05.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.679][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:05.681][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:05.682][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.683][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.685][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:05.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:05.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.689][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:05.691][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:05.692][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.693][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.694][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:05.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:05.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.698][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:05.699][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:05.700][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.701][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.703][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:05.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:05.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.707][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:05.708][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:05.709][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.710][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.711][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:05.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:05.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.715][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:05.716][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:05.717][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.718][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.719][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:05.720][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:05.721][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.722][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.723][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:05.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:05.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.728][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:05.729][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:05.730][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.730][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:05.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:05.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.736][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:05.737][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:05.738][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.739][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.740][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:05.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:05.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.744][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:05.745][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:05.746][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.747][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.748][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:05.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:05.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.751][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.752][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:05.930][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:05.931][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.931][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.933][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:05.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:05.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.936][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:05.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:05.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.940][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:05.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:05.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:05.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:05.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:05.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:05.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:05.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:05.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:05.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:05.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:05.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:05.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:05.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:05.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:05.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:05.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.968][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:05.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:05.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:05.972][self$createEntryFromContent] Accession numbers: 164975. biodb.TRACE[2024-07-06 16:02:05.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:05.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:05.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.976][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:05.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:05.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:05.980][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:05.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:05.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:05.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:05.983][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:05.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:05.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:05.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:05.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:05.990][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:05.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:05.992][private$loadEntries] Creating entries from ids [1]: "164994". biodb.DEBUG[2024-07-06 16:02:05.993][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:05.994][cch$loadFileContent] Trying to load 1 files from cache: [1]: "164994". biodb.TRACE[2024-07-06 16:02:05.996][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:05.996][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:05.997][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:05.998][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:05.999][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:06.000][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:06.002][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:06.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:06.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:06.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:06.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:06.010][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:06.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:06.012][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=164994". biodb.DEBUG[2024-07-06 16:02:06.014][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:06.015][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:06.016][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=164994". biodb.TRACE[2024-07-06 16:02:06.409][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=164994). biodb.DEBUG[2024-07-06 16:02:06.837][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:06.841][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c2789f33696a1a62a1d6cd81e3041cd1.content" biodb.TRACE[2024-07-06 16:02:06.848][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c2789f33696a1a62a1d6cd81e3041cd1.request" biodb.TRACE[2024-07-06 16:02:06.854][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/164994.xml" biodb.DEBUG[2024-07-06 16:02:06.857][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:06.859][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:06.862][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:06.865][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:06.867][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:06.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:06.878][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:06.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:06.881][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:06.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:06.887][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:06.888][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:06.890][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.891][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:06.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:06.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.899][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:06.901][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:06.902][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.903][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.905][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:06.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:06.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.909][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.910][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:06.911][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:06.912][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.913][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.915][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:06.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:06.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.919][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:06.921][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:06.922][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.923][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.924][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:06.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:06.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.928][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:06.929][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:06.930][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.931][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.932][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:06.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:06.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.935][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:06.936][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:06.937][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.938][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.939][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:06.940][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:06.941][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.946][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.950][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:06.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:06.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.953][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:06.954][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:06.955][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.956][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:06.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:06.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.961][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:06.962][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:06.962][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.963][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.964][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:06.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:06.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.968][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:06.969][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:06.970][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.971][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.972][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:06.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:06.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.975][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:06.976][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:06.977][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.978][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.979][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:06.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:06.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:06.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:06.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:06.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:06.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.990][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:06.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:06.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:06.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:06.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:06.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:06.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:06.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:06.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:07.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:07.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:07.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:07.004][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:07.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:07.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:07.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:07.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:07.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:07.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:07.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:07.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.013][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:07.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:07.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:07.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:07.018][self$createEntryFromContent] Accession numbers: 164994. biodb.TRACE[2024-07-06 16:02:07.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:07.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:07.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:07.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:07.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:07.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:07.026][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:07.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:07.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:07.029][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:07.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:07.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:07.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:07.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:07.036][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:07.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:07.038][private$loadEntries] Creating entries from ids [1]: "169251". biodb.DEBUG[2024-07-06 16:02:07.039][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:07.040][cch$loadFileContent] Trying to load 1 files from cache: [1]: "169251". biodb.TRACE[2024-07-06 16:02:07.041][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:07.042][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:07.043][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:07.044][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:07.045][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:07.046][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:07.048][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:07.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:07.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:07.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:07.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:07.056][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:07.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:07.057][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169251". biodb.DEBUG[2024-07-06 16:02:07.060][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:07.061][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:07.062][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169251". biodb.TRACE[2024-07-06 16:02:07.456][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169251). biodb.DEBUG[2024-07-06 16:02:07.896][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:07.900][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/06c85ce8d5c9a410c27ad425a575abe7.content" biodb.TRACE[2024-07-06 16:02:07.907][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/06c85ce8d5c9a410c27ad425a575abe7.request" biodb.TRACE[2024-07-06 16:02:07.913][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/169251.xml" biodb.DEBUG[2024-07-06 16:02:07.915][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:07.918][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:07.921][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:07.924][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:07.926][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:07.928][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:07.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:07.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:07.940][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:07.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:07.946][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:07.948][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:07.949][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.951][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:07.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:07.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:07.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:07.958][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:07.960][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:07.961][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.962][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:07.964][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:07.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:07.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:07.969][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:07.978][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:07.979][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.980][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:07.981][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:07.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:07.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.984][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:07.985][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:07.986][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:07.987][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.988][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:07.989][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:07.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:07.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:07.993][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:07.994][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:07.994][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.995][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:07.996][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:07.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:07.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:07.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.000][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:08.001][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:08.002][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.003][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.004][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:08.005][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:08.006][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.006][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.008][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:08.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:08.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.011][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:08.012][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:08.013][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.014][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:08.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:08.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.018][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:08.019][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:08.020][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.021][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.022][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:08.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:08.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.026][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:08.027][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:08.028][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.029][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.030][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:08.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:08.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.033][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:08.034][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:08.035][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.036][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.037][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:08.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:08.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:08.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:08.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.044][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:08.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:08.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:08.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:08.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:08.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:08.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:08.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:08.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:08.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:08.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.060][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:08.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:08.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:08.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:08.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:08.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:08.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:08.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:08.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:08.075][self$createEntryFromContent] Accession numbers: 169251. biodb.TRACE[2024-07-06 16:02:08.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:08.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:08.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:08.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:08.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:08.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:08.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:08.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:08.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:08.087][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:08.088][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:08.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:08.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:08.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:08.094][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:08.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:08.096][private$loadEntries] Creating entries from ids [1]: "224261". biodb.DEBUG[2024-07-06 16:02:08.097][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:08.098][cch$loadFileContent] Trying to load 1 files from cache: [1]: "224261". biodb.TRACE[2024-07-06 16:02:08.099][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:08.100][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:08.101][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:08.102][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:08.103][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:08.104][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:08.106][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:08.107][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:08.108][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:08.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:08.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:08.114][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:08.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:08.116][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=224261". biodb.DEBUG[2024-07-06 16:02:08.118][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:08.119][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:08.120][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=224261". biodb.TRACE[2024-07-06 16:02:08.511][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=224261). biodb.DEBUG[2024-07-06 16:02:08.942][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:08.947][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7ba99c29fa5d3888a543698650c3997e.content" biodb.TRACE[2024-07-06 16:02:08.953][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7ba99c29fa5d3888a543698650c3997e.request" biodb.TRACE[2024-07-06 16:02:08.959][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/224261.xml" biodb.DEBUG[2024-07-06 16:02:08.962][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:08.976][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:08.978][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:08.982][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:08.984][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:08.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:08.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:08.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:08.997][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:08.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:09.001][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:09.003][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:09.004][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.006][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:09.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:09.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.013][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:09.014][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:09.015][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.016][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.018][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:09.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:09.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.022][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:09.023][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:09.024][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.025][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.027][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:09.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:09.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.031][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:09.032][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:09.033][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.034][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.035][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:09.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:09.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.038][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.039][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:09.039][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:09.040][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.041][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.042][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:09.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:09.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.046][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:09.047][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:09.048][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.048][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.050][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:09.050][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:09.051][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.052][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.053][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:09.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:09.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.057][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:09.058][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:09.059][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.059][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:09.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:09.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.064][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:09.065][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:09.066][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.067][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.068][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:09.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:09.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.071][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:09.072][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:09.073][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.074][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.075][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:09.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:09.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.079][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:09.080][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:09.080][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.081][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.082][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:09.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:09.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:09.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:09.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.090][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:09.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:09.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.093][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:09.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:09.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:09.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:09.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:09.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:09.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:09.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:09.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:09.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:09.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:09.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:09.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:09.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:09.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:09.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:09.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:09.121][self$createEntryFromContent] Accession numbers: 224261. biodb.TRACE[2024-07-06 16:02:09.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:09.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:09.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.126][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:09.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:09.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:09.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:09.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:09.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:09.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:09.134][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:09.137][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:09.138][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:09.139][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:02:09.541][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:02:09.987][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:09.991][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/357534c211a0779cb44e196fcebae6c0.content" biodb.TRACE[2024-07-06 16:02:09.999][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/357534c211a0779cb44e196fcebae6c0.request" biodb.DEBUG[2024-07-06 16:02:10.016][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:10.018][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:10.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:10.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:10.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:10.032][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:10.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:10.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:10.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:10.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:10.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:10.043][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:10.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:10.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:10.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:10.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:10.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:10.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:10.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:10.054][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:10.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:10.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:10.062][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:10.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:10.064][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:10.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:10.066][private$loadEntries] Creating entries from ids [1]: "71954". biodb.DEBUG[2024-07-06 16:02:10.067][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:10.069][cch$loadFileContent] Trying to load 1 files from cache: [1]: "71954". biodb.TRACE[2024-07-06 16:02:10.070][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:10.071][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:10.072][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:10.073][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:10.074][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:10.075][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:10.078][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:10.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:10.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:10.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:10.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:10.085][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:10.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:10.087][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=71954". biodb.DEBUG[2024-07-06 16:02:10.090][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:10.090][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:10.092][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=71954". biodb.TRACE[2024-07-06 16:02:10.488][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=71954). biodb.DEBUG[2024-07-06 16:02:10.938][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:10.942][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/58f24f0de3d9b6c69a2b349522c5c9b3.content" biodb.TRACE[2024-07-06 16:02:10.949][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/58f24f0de3d9b6c69a2b349522c5c9b3.request" biodb.TRACE[2024-07-06 16:02:10.955][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/71954.xml" biodb.DEBUG[2024-07-06 16:02:10.958][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:10.961][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:10.963][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:10.966][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:10.968][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:10.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:10.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:10.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:10.982][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:10.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:10.988][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:10.990][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:10.991][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:10.993][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:10.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:10.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:10.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:10.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.000][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:11.002][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:11.003][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.004][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.006][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:11.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:11.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.011][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:11.012][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:11.013][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.014][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.015][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:11.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:11.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.020][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:11.021][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:11.022][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.023][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:11.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:11.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.028][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:11.029][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:11.029][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.030][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.031][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:11.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:11.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.035][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:11.036][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:11.037][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.038][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.039][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:11.040][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:11.041][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.041][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.043][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:11.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:11.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.046][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:11.047][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:11.048][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.049][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.050][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:11.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:11.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.054][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:11.055][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:11.056][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.056][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.058][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:11.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:11.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.060][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.061][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:11.062][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:11.063][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.064][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.065][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:11.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:11.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.069][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:11.070][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:11.070][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.071][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.072][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:11.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:11.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:11.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:11.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:11.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:11.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:11.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:11.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.093][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:11.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:11.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:11.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:11.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:11.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:11.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:11.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:11.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.108][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:11.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:11.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:11.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:11.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:11.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:11.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:11.118][self$createEntryFromContent] Accession numbers: 71954. biodb.TRACE[2024-07-06 16:02:11.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:11.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:11.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:11.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:11.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:11.126][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:11.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:11.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:11.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:11.130][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:11.130][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:11.131][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:11.135][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:11.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:11.137][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:11.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:11.139][private$loadEntries] Creating entries from ids [1]: "197612". biodb.DEBUG[2024-07-06 16:02:11.139][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:11.141][cch$loadFileContent] Trying to load 1 files from cache: [1]: "197612". biodb.TRACE[2024-07-06 16:02:11.142][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:11.143][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:11.144][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:11.145][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:11.146][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:11.147][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:11.149][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:11.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:11.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:11.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:11.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:11.156][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:11.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:11.158][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=197612". biodb.DEBUG[2024-07-06 16:02:11.160][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:11.161][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:11.163][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=197612". biodb.TRACE[2024-07-06 16:02:11.553][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=197612). biodb.DEBUG[2024-07-06 16:02:11.986][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:11.990][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d602b140c80212c04a1a2ba98ef7dc4f.content" biodb.TRACE[2024-07-06 16:02:11.997][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d602b140c80212c04a1a2ba98ef7dc4f.request" biodb.TRACE[2024-07-06 16:02:12.002][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/197612.xml" biodb.DEBUG[2024-07-06 16:02:12.005][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:12.008][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:12.010][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:12.014][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:12.016][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:12.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:12.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:12.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:12.030][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:12.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:12.035][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:12.037][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:12.038][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.040][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.042][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:12.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:12.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.048][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:12.049][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:12.050][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.051][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.053][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:12.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:12.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.058][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:12.059][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:12.061][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.062][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.063][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:12.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:12.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.068][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:12.069][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:12.070][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.071][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.072][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:12.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:12.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.076][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:12.077][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:12.078][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.079][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.080][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:12.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:12.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.083][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:12.084][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:12.085][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.086][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.087][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:12.088][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:12.089][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.090][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.091][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:12.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:12.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.102][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.103][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.104][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.104][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.109][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:12.110][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:12.111][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.112][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:12.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:12.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.117][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:12.117][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:12.118][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.119][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.120][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:12.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:12.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.124][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:12.125][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:12.126][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.126][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.128][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:12.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:12.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:12.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:12.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:12.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:12.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:12.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:12.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:12.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:12.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:12.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:12.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.159][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:12.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:12.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:12.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:12.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:12.166][self$createEntryFromContent] Accession numbers: 197612. biodb.TRACE[2024-07-06 16:02:12.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:12.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:12.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:12.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:12.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.174][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:12.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:12.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:12.178][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:12.180][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:12.180][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:12.181][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:12.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:12.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:12.187][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:12.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:12.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.195][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.196][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.197][private$selectFields] biodb.TRACE[2024-07-06 16:02:12.197][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:12.198][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:12.199][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.200][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.201][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.202][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.203][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.203][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.204][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.205][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.206][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.207][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.208][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.209][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.210][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.211][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.211][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.212][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:12.213][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.224][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-07-06 16:02:12.225][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:12.226][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:12.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:12.231][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:12.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:12.233][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:12.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:12.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.242][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.243][private$selectFields] biodb.TRACE[2024-07-06 16:02:12.244][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:12.245][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:12.246][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.247][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.247][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.248][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.249][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.250][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.251][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.252][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.257][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.258][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.259][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.259][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.260][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.261][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.262][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.263][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:12.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.274][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [71954]. biodb.DEBUG[2024-07-06 16:02:12.275][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:12.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:12.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:12.281][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:12.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:12.283][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:12.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:12.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.291][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.292][private$selectFields] biodb.TRACE[2024-07-06 16:02:12.293][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:12.294][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:12.295][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.295][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.296][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.297][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.298][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.299][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.300][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.301][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.302][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.302][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.303][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.304][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.305][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.306][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.307][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.308][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:12.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.319][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [197612]. biodb.DEBUG[2024-07-06 16:02:12.320][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:12.321][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-07-06 16:02:12.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.332][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.334][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.339][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.342][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.352][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.360][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.363][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:12.422][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:12.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:12.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:12.428][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:12.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:12.429][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:12.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:12.433][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:12.435][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:12.437][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2024-07-06 16:02:12.438][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:12.439][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2024-07-06 16:02:12.442][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:12.445][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:12.446][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2024-07-06 16:02:12.447][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:12.448][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2024-07-06 16:02:12.451][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:12.451][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:12.452][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:12.456][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:12.457][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:12.458][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:12.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:12.460][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.462][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.463][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.466][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.467][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:12.470][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:12.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:12.472][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:12.476][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:12.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:12.477][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:12.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:12.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:12.490][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:12.491][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:12.491][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:12.495][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:12.496][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:12.497][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:12.498][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:12.499][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.502][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.505][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:12.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:12.509][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:12.511][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:12.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:12.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:12.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:12.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:12.518][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:12.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:12.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.527][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.528][private$selectFields] biodb.TRACE[2024-07-06 16:02:12.529][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:12.530][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:12.531][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.531][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.532][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.533][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.534][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.535][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.536][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.537][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.538][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.538][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.539][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.540][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.541][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.542][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.543][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.544][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:12.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.548][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.560][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2024-07-06 16:02:12.561][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:12.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:12.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:12.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:12.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:12.568][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:12.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:12.580][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.606][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.607][private$selectFields] biodb.TRACE[2024-07-06 16:02:12.607][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:12.608][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:12.609][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.610][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.611][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.612][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.613][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.614][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.614][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.615][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.616][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.617][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.626][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.627][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.628][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.629][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.630][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.630][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:12.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.635][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.642][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-07-06 16:02:12.643][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:12.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:12.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:12.649][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:12.650][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:12.650][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:12.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:12.652][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.655][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.659][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.660][private$selectFields] biodb.TRACE[2024-07-06 16:02:12.661][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:12.662][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:12.663][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.664][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.665][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.666][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.666][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.667][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.668][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.669][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.670][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.671][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.672][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:12.673][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.674][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.674][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.675][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.676][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:12.677][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:12.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:12.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:12.688][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2024-07-06 16:02:12.689][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:12.690][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:02:12.692][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:12.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:12.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:12.701][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:12.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:12.703][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:12.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:12.706][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.29*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:12.709][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:12.710][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:12.711][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.29%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:02:13.103][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.29%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:02:13.514][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:13.518][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7269bbea581f1e243800f8ee4e0f4fdb.content" biodb.TRACE[2024-07-06 16:02:13.526][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7269bbea581f1e243800f8ee4e0f4fdb.request" biodb.DEBUG[2024-07-06 16:02:13.531][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:13.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:13.535][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:13.544][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:13.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:13.548][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:13.550][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:13.552][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:13.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:13.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:13.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:13.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:13.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:13.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:13.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:13.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:13.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:13.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:13.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:13.572][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:13.574][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:13.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:13.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:13.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:13.583][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:13.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:13.585][private$loadEntries] Creating entries from ids [1]: "91601". biodb.DEBUG[2024-07-06 16:02:13.587][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:13.588][cch$loadFileContent] Trying to load 1 files from cache: [1]: "91601". biodb.TRACE[2024-07-06 16:02:13.590][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:13.591][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:13.592][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:13.593][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:13.594][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:13.595][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:13.598][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:13.599][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:13.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:13.604][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:13.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:13.606][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:13.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:13.607][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=91601". biodb.DEBUG[2024-07-06 16:02:13.610][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:13.611][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:13.612][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=91601". biodb.TRACE[2024-07-06 16:02:14.019][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=91601). biodb.DEBUG[2024-07-06 16:02:14.450][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:14.454][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aa7bc0b3048e5fb322307698a3f56fa6.content" biodb.TRACE[2024-07-06 16:02:14.461][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aa7bc0b3048e5fb322307698a3f56fa6.request" biodb.TRACE[2024-07-06 16:02:14.466][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/91601.xml" biodb.DEBUG[2024-07-06 16:02:14.469][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:14.472][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:14.474][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:14.478][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:14.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:14.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:14.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:14.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:14.494][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:14.496][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:14.500][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:14.502][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:14.504][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.505][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.507][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:14.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:14.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.513][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:14.515][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:14.516][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.517][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.519][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:14.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:14.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.524][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:14.525][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:14.526][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.527][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.529][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:14.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:14.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.533][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:14.534][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:14.535][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.536][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:14.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:14.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.541][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:14.542][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:14.543][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.544][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:14.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:14.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.549][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:14.550][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:14.551][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.552][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.553][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:14.554][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:14.555][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.556][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.557][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:14.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:14.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.561][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:14.561][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:14.562][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.573][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:14.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:14.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.578][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:14.579][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:14.580][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.581][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:14.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:14.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.585][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:14.586][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:14.587][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.588][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.589][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:14.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:14.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.592][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.593][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:14.594][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:14.594][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.595][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.596][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:14.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:14.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:14.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:14.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.604][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:14.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:14.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:14.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:14.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:14.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:14.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:14.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:14.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.618][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:14.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:14.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:14.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:14.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:14.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:14.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:14.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:14.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:14.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:14.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:14.635][self$createEntryFromContent] Accession numbers: 91601. biodb.TRACE[2024-07-06 16:02:14.636][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:14.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:14.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.639][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.640][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:14.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:14.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.642][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:14.643][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:14.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:14.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:14.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:14.647][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:14.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:14.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:14.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:14.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:14.654][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:14.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:14.656][private$loadEntries] Creating entries from ids [1]: "95147". biodb.DEBUG[2024-07-06 16:02:14.656][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:14.658][cch$loadFileContent] Trying to load 1 files from cache: [1]: "95147". biodb.TRACE[2024-07-06 16:02:14.659][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:14.660][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:14.661][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:14.662][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:14.663][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:14.664][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:14.666][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:14.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:14.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:14.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:14.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:14.673][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:14.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:14.675][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=95147". biodb.DEBUG[2024-07-06 16:02:14.677][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:14.678][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:14.679][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=95147". biodb.TRACE[2024-07-06 16:02:15.081][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=95147). biodb.DEBUG[2024-07-06 16:02:15.510][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:15.514][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d5dbc153d74635342b8ea0e83790c39e.content" biodb.TRACE[2024-07-06 16:02:15.521][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d5dbc153d74635342b8ea0e83790c39e.request" biodb.TRACE[2024-07-06 16:02:15.526][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/95147.xml" biodb.DEBUG[2024-07-06 16:02:15.529][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:15.532][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:15.534][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:15.538][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:15.540][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:15.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:15.551][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:15.553][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:15.554][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:15.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:15.559][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:15.561][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:15.563][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.564][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:15.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:15.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.572][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:15.573][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:15.575][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.576][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.578][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:15.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:15.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.583][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:15.584][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:15.585][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.586][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.588][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:15.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:15.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.600][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:15.601][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:15.602][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.603][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.604][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:15.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:15.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.607][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:15.608][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:15.609][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.610][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.611][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:15.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:15.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.615][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:15.616][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:15.616][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.617][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.618][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:15.619][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:15.620][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.621][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.622][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:15.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:15.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.626][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:15.627][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:15.627][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.628][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:15.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:15.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.633][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:15.634][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:15.635][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.636][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.637][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:15.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:15.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.639][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.640][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:15.641][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:15.642][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.643][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.644][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:15.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:15.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.648][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:15.649][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:15.649][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.650][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.651][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:15.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:15.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.655][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.658][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.661][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:15.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:15.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:15.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:15.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:15.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:15.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:15.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:15.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:15.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:15.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:15.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:15.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.687][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:15.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:15.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:15.690][self$createEntryFromContent] Accession numbers: 95147. biodb.TRACE[2024-07-06 16:02:15.691][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:15.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:15.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.695][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:15.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:15.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:15.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:15.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:15.702][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:15.703][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:15.704][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:15.705][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:15.709][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:15.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:15.711][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:15.711][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:15.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.715][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.720][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:15.721][private$selectFields] biodb.TRACE[2024-07-06 16:02:15.722][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:15.722][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:15.723][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:15.724][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.725][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.726][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.727][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.728][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.729][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.730][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.730][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.731][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:15.732][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:15.733][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.734][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.735][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.736][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.737][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:15.737][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.740][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.745][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.752][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-07-06 16:02:15.753][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:15.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:15.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:15.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:15.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:15.760][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:15.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:15.762][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.769][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:15.770][private$selectFields] biodb.TRACE[2024-07-06 16:02:15.771][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:15.772][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:15.772][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:15.773][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.774][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.775][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.776][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.777][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.778][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.779][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.779][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.780][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:15.781][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:15.782][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.783][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.784][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.785][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.785][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:15.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.797][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [91601]. biodb.DEBUG[2024-07-06 16:02:15.798][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:15.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:15.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:15.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:15.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:15.805][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:15.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:15.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.814][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:15.815][private$selectFields] biodb.TRACE[2024-07-06 16:02:15.816][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:15.816][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:15.817][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:15.818][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.819][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.820][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.821][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.822][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.822][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.823][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.824][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.825][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:15.826][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:15.827][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.828][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.828][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.829][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.830][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:15.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:15.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:15.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:15.842][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [95147]. biodb.DEBUG[2024-07-06 16:02:15.843][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:15.844][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:02:15.845][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:15.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:15.847][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:15.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:15.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:15.852][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:15.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:15.856][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:15.858][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:15.859][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:15.861][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:02:16.249][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:02:16.671][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:16.675][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/acfa4b558978abf12409c2b56e678d03.content" biodb.TRACE[2024-07-06 16:02:16.683][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/acfa4b558978abf12409c2b56e678d03.request" biodb.DEBUG[2024-07-06 16:02:16.690][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:16.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:16.694][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:16.703][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:16.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:16.707][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:16.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:16.711][private$loadEntries] Creating entries from ids [1]: "636". biodb.DEBUG[2024-07-06 16:02:16.713][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:16.716][cch$loadFileContent] Trying to load 1 files from cache: [1]: "636". biodb.TRACE[2024-07-06 16:02:16.719][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:16.721][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:16.722][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:16.724][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:16.726][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:16.727][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:16.731][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:16.733][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:16.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:16.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:16.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:16.742][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:16.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:16.745][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=636". biodb.DEBUG[2024-07-06 16:02:16.756][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:16.757][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:16.759][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=636". biodb.TRACE[2024-07-06 16:02:17.167][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=636). biodb.DEBUG[2024-07-06 16:02:17.603][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:17.607][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ccb008951a89970d7f0e2dfe6ae3860d.content" biodb.TRACE[2024-07-06 16:02:17.614][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ccb008951a89970d7f0e2dfe6ae3860d.request" biodb.TRACE[2024-07-06 16:02:17.619][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/636.xml" biodb.DEBUG[2024-07-06 16:02:17.622][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:17.625][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:17.627][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:17.630][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:17.632][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:17.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:17.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:17.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:17.647][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:17.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:17.652][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:17.654][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:17.656][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.657][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:17.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:17.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.664][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.665][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:17.667][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:17.668][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.669][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.671][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:17.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:17.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.674][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.675][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:17.677][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:17.678][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.679][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.680][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:17.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:17.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.685][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:17.686][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:17.687][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.688][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.689][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:17.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:17.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.692][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.693][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:17.694][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:17.695][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.695][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.697][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:17.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:17.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.700][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:17.701][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:17.702][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.703][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.704][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:17.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:17.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.707][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:17.708][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:17.709][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.710][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.711][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:17.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:17.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.715][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:17.716][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:17.716][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.717][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:17.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:17.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.722][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:17.723][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:17.724][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.724][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.726][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:17.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:17.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.729][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:17.730][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:17.731][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.732][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.733][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:17.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:17.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.736][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:17.737][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:17.738][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.739][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.740][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:17.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:17.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:17.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:17.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:17.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:17.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:17.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:17.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:17.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:17.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:17.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:17.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:17.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:17.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:17.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:17.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:17.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:17.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:17.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:17.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:17.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:17.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:17.779][self$createEntryFromContent] Accession numbers: 636. biodb.TRACE[2024-07-06 16:02:17.780][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:17.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:17.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:17.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:17.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:17.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:17.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:17.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:17.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:17.798][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:17.799][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:17.800][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:17.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:17.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:17.805][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:17.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:17.807][private$loadEntries] Creating entries from ids [1]: "64199". biodb.DEBUG[2024-07-06 16:02:17.808][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:17.809][cch$loadFileContent] Trying to load 1 files from cache: [1]: "64199". biodb.TRACE[2024-07-06 16:02:17.810][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:17.811][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:17.812][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:17.813][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:17.814][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:17.815][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:17.817][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:17.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:17.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:17.823][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:17.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:17.824][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:17.825][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:17.826][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64199". biodb.DEBUG[2024-07-06 16:02:17.828][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:17.829][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:17.831][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64199". biodb.TRACE[2024-07-06 16:02:18.223][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64199). biodb.DEBUG[2024-07-06 16:02:18.656][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:18.661][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a31cc2b07404761abdda19d4ffeaa880.content" biodb.TRACE[2024-07-06 16:02:18.668][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a31cc2b07404761abdda19d4ffeaa880.request" biodb.TRACE[2024-07-06 16:02:18.673][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64199.xml" biodb.DEBUG[2024-07-06 16:02:18.676][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:18.678][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:18.681][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:18.684][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:18.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:18.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:18.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:18.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:18.700][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:18.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:18.706][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:18.708][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:18.709][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.711][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:18.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:18.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.718][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:18.720][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:18.721][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.722][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.724][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:18.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:18.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.729][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:18.730][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:18.731][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.732][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.734][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:18.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:18.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.738][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:18.739][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:18.740][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.741][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.742][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:18.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:18.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.746][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:18.747][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:18.748][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.749][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:18.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:18.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.754][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:18.755][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:18.755][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.756][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.757][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:18.758][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:18.759][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.760][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.761][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:18.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:18.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.765][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:18.766][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:18.766][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.767][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:18.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:18.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.772][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:18.773][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:18.774][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.775][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.776][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:18.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:18.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.780][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:18.781][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:18.781][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.782][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.783][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:18.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:18.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.787][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:18.788][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:18.789][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.790][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.791][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:18.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:18.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.793][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:18.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:18.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.798][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:18.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:18.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.802][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:18.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:18.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.804][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:18.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:18.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.816][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:18.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:18.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:18.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:18.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:18.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:18.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:18.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:18.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:18.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:18.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:18.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:18.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:18.838][self$createEntryFromContent] Accession numbers: 64199. biodb.TRACE[2024-07-06 16:02:18.839][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:18.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:18.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.842][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:18.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:18.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:18.846][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:18.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:18.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:18.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:18.849][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:18.850][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:18.851][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:18.855][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:18.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:18.857][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:18.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:18.858][private$loadEntries] Creating entries from ids [1]: "65648". biodb.DEBUG[2024-07-06 16:02:18.859][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:18.861][cch$loadFileContent] Trying to load 1 files from cache: [1]: "65648". biodb.TRACE[2024-07-06 16:02:18.862][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:18.863][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:18.864][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:18.865][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:18.866][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:18.866][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:18.869][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:18.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:18.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:18.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:18.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:18.876][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:18.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:18.878][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65648". biodb.DEBUG[2024-07-06 16:02:18.880][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:18.881][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:18.882][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65648". biodb.TRACE[2024-07-06 16:02:19.283][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65648). biodb.DEBUG[2024-07-06 16:02:19.719][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:19.723][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4176d017d73a3b7cdd77f889aa9b1b1d.content" biodb.TRACE[2024-07-06 16:02:19.730][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4176d017d73a3b7cdd77f889aa9b1b1d.request" biodb.TRACE[2024-07-06 16:02:19.736][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65648.xml" biodb.DEBUG[2024-07-06 16:02:19.738][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:19.741][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:19.743][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:19.747][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:19.749][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:19.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:19.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:19.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:19.763][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:19.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:19.769][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:19.771][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:19.772][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.774][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:19.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:19.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.782][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:19.783][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:19.784][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.786][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.787][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:19.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:19.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.792][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:19.793][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:19.795][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.796][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.797][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:19.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:19.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.800][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.801][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:19.803][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:19.804][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.804][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.806][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:19.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:19.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.810][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:19.811][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:19.812][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.812][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.814][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:19.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:19.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.817][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:19.818][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:19.819][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.820][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.821][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:19.822][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:19.823][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.824][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.825][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:19.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:19.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.828][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:19.829][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:19.830][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.831][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:19.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:19.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.836][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:19.837][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:19.842][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.846][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:19.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:19.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.851][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:19.851][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:19.852][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.853][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.854][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:19.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:19.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.858][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:19.859][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:19.859][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.860][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.861][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:19.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:19.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:19.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:19.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.878][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.879][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:19.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:19.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:19.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:19.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:19.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:19.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:19.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:19.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.893][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:19.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:19.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.896][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.896][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:19.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:19.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:19.900][self$createEntryFromContent] Accession numbers: 65648. biodb.TRACE[2024-07-06 16:02:19.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:19.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:19.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:19.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:19.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:19.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:19.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:19.911][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:19.913][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:19.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:19.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:19.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:19.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:19.920][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:19.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:19.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.924][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.929][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:19.930][private$selectFields] biodb.TRACE[2024-07-06 16:02:19.931][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:19.931][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:19.932][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:19.933][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.934][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.935][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.936][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.937][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.937][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.938][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.939][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.944][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:19.946][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:19.947][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.948][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.949][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.950][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.951][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:19.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.956][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.960][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.963][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.965][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [636]. biodb.DEBUG[2024-07-06 16:02:19.966][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:19.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:19.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:19.974][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:19.976][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:19.977][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:19.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:19.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.983][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.987][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:19.988][private$selectFields] biodb.TRACE[2024-07-06 16:02:19.989][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:19.990][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:19.991][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:19.992][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.994][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.995][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.996][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:19.997][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.998][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:19.999][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:19.999][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.001][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.002][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.003][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.004][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.005][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.005][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.006][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:20.008][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.024][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.028][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.032][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [64199]. biodb.DEBUG[2024-07-06 16:02:20.033][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.034][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.035][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.041][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.047][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.050][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.051][private$selectFields] biodb.TRACE[2024-07-06 16:02:20.052][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:20.053][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:20.054][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.055][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.056][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.057][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.058][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.059][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.060][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.061][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.062][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.063][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.063][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.064][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.065][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.066][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.067][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.068][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:20.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.081][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [65648]. biodb.DEBUG[2024-07-06 16:02:20.082][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:20.083][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-07-06 16:02:20.090][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-07-06 16:02:20.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-07-06 16:02:20.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.094][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-07-06 16:02:20.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-07-06 16:02:20.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.098][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-07-06 16:02:20.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-07-06 16:02:20.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.101][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-07-06 16:02:20.105][biodb::testThat] biodb.INFO [2024-07-06 16:02:20.106][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() "). biodb.INFO [2024-07-06 16:02:20.106][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-07-06 16:02:20.107][biodb::testThat] biodb.TRACE[2024-07-06 16:02:20.110][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-07-06 16:02:20.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-07-06 16:02:20.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.114][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-07-06 16:02:20.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-07-06 16:02:20.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.118][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-07-06 16:02:20.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-07-06 16:02:20.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.122][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.140][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.142][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.143][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.147][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.154][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.157][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:20.167][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.174][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:20.178][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:20.185][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:20.186][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-07-06 16:02:20.187][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:20.188][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-07-06 16:02:20.190][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.196][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.197][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.199][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:20.210][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:20.213][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:20.214][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-07-06 16:02:20.215][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:20.217][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-07-06 16:02:20.219][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.224][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.226][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.231][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:20.238][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.244][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.245][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:20.258][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:20.259][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.264][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.265][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.266][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.275][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.276][private$selectFields] biodb.TRACE[2024-07-06 16:02:20.277][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:20.277][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:20.278][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.279][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.280][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.281][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.282][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.283][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.284][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.284][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.285][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.286][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.287][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.288][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.289][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.290][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.290][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.291][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:20.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.303][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288]. biodb.DEBUG[2024-07-06 16:02:20.304][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.311][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.313][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.316][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.317][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.320][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.321][private$selectFields] biodb.TRACE[2024-07-06 16:02:20.322][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:20.323][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:20.324][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.325][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.326][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.327][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.327][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.328][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.329][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.330][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.331][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.336][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.337][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.338][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.339][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.340][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.341][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.341][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:20.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.352][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.353][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-07-06 16:02:20.354][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.355][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.356][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.360][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.360][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.361][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.370][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.371][private$selectFields] biodb.TRACE[2024-07-06 16:02:20.372][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:20.372][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:20.373][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.374][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.375][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.376][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.377][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.378][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.379][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.379][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.380][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.381][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.382][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.383][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.384][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.385][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.385][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.386][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:20.387][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.391][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.394][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.398][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892]. biodb.DEBUG[2024-07-06 16:02:20.399][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:20.399][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:02:20.401][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.407][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.408][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:20.412][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:20.414][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:20.416][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b3cd8ddf08f509014f10dc9bf7c1649d". biodb.TRACE[2024-07-06 16:02:20.417][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:20.418][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b3cd8ddf08f509014f10dc9bf7c1649d.content". biodb.DEBUG[2024-07-06 16:02:20.420][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.425][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.427][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.436][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:20.439][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.440][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.441][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.445][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.447][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.455][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.455][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:20.460][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:20.463][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:20.464][cch$loadFileContent] Trying to load 1 files from cache: [1]: "831507e33c6cf42061851262412f5feb". biodb.TRACE[2024-07-06 16:02:20.465][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:20.466][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/831507e33c6cf42061851262412f5feb.content". biodb.DEBUG[2024-07-06 16:02:20.469][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.469][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.474][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.476][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.485][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:20.497][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.498][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.502][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.503][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.504][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:20.516][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.517][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.522][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.523][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.525][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.528][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:20.536][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:20.537][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.544][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.550][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.553][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.554][private$selectFields] biodb.TRACE[2024-07-06 16:02:20.555][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:20.556][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:20.557][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.558][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.559][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.559][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.560][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.561][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.562][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.563][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.564][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.565][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.565][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.566][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.567][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.568][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.569][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.570][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:20.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.582][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-07-06 16:02:20.583][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.583][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.590][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.592][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.599][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.600][private$selectFields] biodb.TRACE[2024-07-06 16:02:20.601][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:20.601][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:20.602][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.603][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.604][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.605][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.606][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.607][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.608][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.609][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.610][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.611][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.612][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.612][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.613][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.614][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.615][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.616][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:20.617][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.621][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.628][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-07-06 16:02:20.629][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.637][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.645][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.650][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.651][private$selectFields] biodb.TRACE[2024-07-06 16:02:20.652][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:20.653][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:20.654][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.655][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.656][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.657][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.657][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.658][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.659][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.660][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.661][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.662][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.663][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:20.664][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.664][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.665][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.666][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.667][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:20.668][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.671][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.674][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:20.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.679][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [19804]. biodb.DEBUG[2024-07-06 16:02:20.680][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:20.680][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:02:20.682][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.688][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.689][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:20.693][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:20.695][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:20.697][cch$loadFileContent] Trying to load 1 files from cache: [1]: "357534c211a0779cb44e196fcebae6c0". biodb.TRACE[2024-07-06 16:02:20.698][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:20.699][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/357534c211a0779cb44e196fcebae6c0.content". biodb.DEBUG[2024-07-06 16:02:20.701][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.708][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.710][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.716][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.717][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:20.721][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.728][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.732][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.739][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:20.740][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:20.741][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:20.742][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:20.746][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:20.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:20.748][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:20.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:20.749][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.753][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:20.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:20.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:20.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:20.761][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.4*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:20.763][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:20.764][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:20.766][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.4%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:02:21.169][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.4%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:02:21.744][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:21.747][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dd9d19fb78fcc7453eff2e9dd7ba5702.content" biodb.TRACE[2024-07-06 16:02:21.752][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dd9d19fb78fcc7453eff2e9dd7ba5702.request" biodb.DEBUG[2024-07-06 16:02:21.761][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:21.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:21.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:21.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:21.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:21.775][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:21.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:21.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:21.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:21.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:21.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:21.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:21.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:21.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:21.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:21.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:21.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:21.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:21.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:21.800][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:21.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:21.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:21.819][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:21.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:21.822][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:21.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:21.824][private$loadEntries] Creating entries from ids [1]: "3017". biodb.DEBUG[2024-07-06 16:02:21.826][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:21.828][cch$loadFileContent] Trying to load 1 files from cache: [1]: "3017". biodb.TRACE[2024-07-06 16:02:21.830][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:21.831][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:21.832][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:21.834][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:21.835][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:21.836][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:21.840][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:21.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:21.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:21.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:21.849][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:21.851][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:21.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:21.853][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3017". biodb.DEBUG[2024-07-06 16:02:21.857][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:21.858][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:21.860][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3017". biodb.TRACE[2024-07-06 16:02:22.263][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3017). biodb.DEBUG[2024-07-06 16:02:22.702][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:22.707][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a0d2dadbafdef2154bb32b0db7e287ac.content" biodb.TRACE[2024-07-06 16:02:22.714][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a0d2dadbafdef2154bb32b0db7e287ac.request" biodb.TRACE[2024-07-06 16:02:22.719][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/3017.xml" biodb.DEBUG[2024-07-06 16:02:22.722][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:22.724][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:22.727][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:22.730][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:22.732][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:22.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:22.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:22.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:22.746][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:22.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:22.752][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:22.753][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:22.755][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.756][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:22.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:22.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.764][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:22.765][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:22.767][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.768][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.770][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:22.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:22.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.775][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:22.776][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:22.777][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.778][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.779][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:22.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:22.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.784][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:22.785][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:22.786][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.787][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:22.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:22.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.792][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:22.793][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:22.794][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.794][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.795][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:22.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:22.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.799][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:22.800][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:22.801][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.802][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.803][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:22.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:22.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.806][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:22.807][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:22.808][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.809][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.810][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:22.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:22.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.814][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:22.815][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:22.815][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.816][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:22.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:22.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.820][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.821][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:22.822][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:22.823][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.824][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.825][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:22.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:22.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.829][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:22.829][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:22.830][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.831][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.832][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:22.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:22.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.836][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:22.837][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:22.838][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.839][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.840][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:22.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:22.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:22.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:22.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:22.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:22.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:22.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:22.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.854][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:22.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:22.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.858][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:22.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:22.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:22.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:22.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:22.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:22.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:22.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:22.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:22.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:22.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:22.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:22.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:22.887][self$createEntryFromContent] Accession numbers: 3017. biodb.TRACE[2024-07-06 16:02:22.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:22.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:22.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:22.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:22.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:22.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:22.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:22.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:22.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:22.898][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:22.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:22.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:22.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:22.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:22.905][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:22.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:22.907][private$loadEntries] Creating entries from ids [1]: "3510". biodb.DEBUG[2024-07-06 16:02:22.908][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:22.909][cch$loadFileContent] Trying to load 1 files from cache: [1]: "3510". biodb.TRACE[2024-07-06 16:02:22.910][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:22.911][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:22.912][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:22.913][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:22.914][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:22.915][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:22.917][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:22.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:22.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:22.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:22.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:22.925][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:22.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:22.927][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3510". biodb.DEBUG[2024-07-06 16:02:22.929][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:22.930][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:22.931][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3510". biodb.TRACE[2024-07-06 16:02:23.337][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3510). biodb.DEBUG[2024-07-06 16:02:23.768][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:23.772][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/58362fa70b44eecb6a87afbf9b6dfd8b.content" biodb.TRACE[2024-07-06 16:02:23.777][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/58362fa70b44eecb6a87afbf9b6dfd8b.request" biodb.TRACE[2024-07-06 16:02:23.781][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/3510.xml" biodb.DEBUG[2024-07-06 16:02:23.783][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:23.785][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:23.787][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:23.790][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:23.791][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:23.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:23.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:23.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:23.803][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:23.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:23.808][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:23.810][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:23.811][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.813][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:23.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:23.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.820][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:23.822][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:23.823][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.824][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.826][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:23.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:23.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.831][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:23.832][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:23.833][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.834][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.836][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:23.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:23.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.840][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:23.841][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:23.842][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.843][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.844][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:23.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:23.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.848][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:23.849][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:23.850][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.851][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.852][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:23.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:23.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.856][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:23.857][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:23.858][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.858][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.860][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:23.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:23.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.863][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:23.864][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:23.865][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.866][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.867][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:23.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:23.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.871][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:23.871][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:23.872][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.873][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.874][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:23.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:23.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.878][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:23.879][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:23.880][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.881][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.882][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:23.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:23.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.893][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:23.894][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:23.895][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.896][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.897][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:23.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:23.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.900][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:23.901][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:23.902][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.903][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.904][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:23.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:23.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.908][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:23.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:23.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.911][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:23.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:23.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:23.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:23.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:23.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:23.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:23.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:23.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.924][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:23.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:23.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:23.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:23.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:23.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:23.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:23.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:23.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:23.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:23.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:23.943][self$createEntryFromContent] Accession numbers: 3510. biodb.TRACE[2024-07-06 16:02:23.943][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:23.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:23.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.947][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:23.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:23.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:23.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:23.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:23.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:23.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:23.954][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:23.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:23.955][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:23.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:23.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:23.961][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:23.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:23.963][private$loadEntries] Creating entries from ids [1]: "7554". biodb.DEBUG[2024-07-06 16:02:23.964][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:23.965][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7554". biodb.TRACE[2024-07-06 16:02:23.966][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:23.967][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:23.968][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:23.969][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:23.970][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:23.971][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:23.973][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:23.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:23.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:23.978][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:23.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:23.980][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:23.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:23.982][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7554". biodb.DEBUG[2024-07-06 16:02:23.984][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:23.985][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:23.986][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7554". biodb.TRACE[2024-07-06 16:02:24.375][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7554). biodb.DEBUG[2024-07-06 16:02:24.807][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:24.811][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66bd6c2472b2485e58ad424b4505cbea.content" biodb.TRACE[2024-07-06 16:02:24.818][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66bd6c2472b2485e58ad424b4505cbea.request" biodb.TRACE[2024-07-06 16:02:24.824][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7554.xml" biodb.DEBUG[2024-07-06 16:02:24.827][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:24.829][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:24.832][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:24.835][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:24.837][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:24.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:24.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:24.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:24.852][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:24.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:24.857][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:24.859][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:24.861][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.862][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:24.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:24.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.870][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:24.872][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:24.873][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.874][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.876][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:24.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:24.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.881][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:24.882][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:24.883][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.884][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.886][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:24.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:24.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.890][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:24.891][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:24.892][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.893][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.894][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:24.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:24.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.906][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:24.907][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:24.908][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.909][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:24.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:24.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.914][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:24.915][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:24.916][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.916][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.918][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:24.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:24.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.921][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:24.922][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:24.923][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.924][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.925][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:24.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:24.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.928][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:24.929][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:24.930][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.931][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.932][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:24.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:24.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.935][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:24.936][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:24.937][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.938][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.939][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:24.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:24.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.943][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:24.944][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:24.945][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.945][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.946][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:24.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:24.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.950][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:24.951][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:24.952][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.952][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.954][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:24.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:24.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:24.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:24.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:24.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:24.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.963][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:24.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:24.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:24.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:24.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:24.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:24.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:24.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:24.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.977][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:24.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:24.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.982][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:24.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:24.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.984][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:24.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:24.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:24.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:24.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:24.992][self$createEntryFromContent] Accession numbers: 7554. biodb.TRACE[2024-07-06 16:02:24.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:24.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:24.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:24.996][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:24.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:24.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:24.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:25.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:25.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:25.003][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:25.005][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:25.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:25.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:25.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:25.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:25.012][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:25.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:25.014][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.017][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.021][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.022][private$selectFields] biodb.TRACE[2024-07-06 16:02:25.022][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:25.023][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:25.024][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.025][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.026][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.027][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.028][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.029][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.030][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.030][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.031][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.032][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.033][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.034][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.035][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.036][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.036][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.037][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:25.038][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.042][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.049][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-07-06 16:02:25.050][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:25.051][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:25.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:25.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:25.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:25.062][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:25.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:25.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.071][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.071][private$selectFields] biodb.TRACE[2024-07-06 16:02:25.072][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:25.073][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:25.074][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.075][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.076][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.076][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.077][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.078][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.079][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.080][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.081][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.082][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.082][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.083][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.084][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.085][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.086][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.087][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:25.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.098][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [3017]. biodb.DEBUG[2024-07-06 16:02:25.099][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:25.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:25.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:25.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:25.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:25.106][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:25.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:25.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.111][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.115][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.116][private$selectFields] biodb.TRACE[2024-07-06 16:02:25.117][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:25.117][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:25.118][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.119][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.120][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.121][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.122][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.123][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.123][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.124][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.125][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.126][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.127][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.128][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.129][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.129][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.130][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.131][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:25.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.142][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.143][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7554]. biodb.DEBUG[2024-07-06 16:02:25.144][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:25.144][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-07-06 16:02:25.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.162][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.165][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.180][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.183][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.187][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:25.196][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:25.197][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:25.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:25.202][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:25.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:25.203][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:25.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:25.211][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:25.214][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:25.215][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2024-07-06 16:02:25.216][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:25.217][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2024-07-06 16:02:25.220][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:25.223][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:25.224][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2024-07-06 16:02:25.225][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:25.226][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2024-07-06 16:02:25.228][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:25.229][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:25.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:25.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:25.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:25.235][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:25.236][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:25.237][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:25.248][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:25.249][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:25.249][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:25.253][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:25.254][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:25.255][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:25.256][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:25.257][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.264][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:25.267][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:25.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:25.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:25.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:25.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:25.274][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:25.275][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:25.276][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:25.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:25.287][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:25.288][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:25.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:25.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:25.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:25.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:25.295][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:25.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:25.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.304][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.305][private$selectFields] biodb.TRACE[2024-07-06 16:02:25.306][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:25.307][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:25.307][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.308][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.309][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.310][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.311][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.312][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.313][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.314][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.314][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.315][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.316][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.317][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.318][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.319][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.320][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.320][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:25.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.332][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2024-07-06 16:02:25.333][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:25.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:25.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:25.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:25.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:25.341][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:25.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:25.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.350][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.351][private$selectFields] biodb.TRACE[2024-07-06 16:02:25.351][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:25.352][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:25.353][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.354][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.355][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.356][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.357][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.358][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.359][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.364][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.365][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.366][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.367][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.368][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.369][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.370][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.371][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.372][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:25.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.384][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-07-06 16:02:25.384][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:25.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:25.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:25.390][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:25.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:25.392][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:25.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:25.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.397][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.400][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.400][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.401][private$selectFields] biodb.TRACE[2024-07-06 16:02:25.402][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:25.403][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:25.404][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.405][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.405][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.406][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.407][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.408][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.409][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.410][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.411][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.411][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.412][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:25.413][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.414][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.415][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.416][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.417][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:25.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:25.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:25.427][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:25.428][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2024-07-06 16:02:25.429][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:25.430][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:02:25.432][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:25.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:25.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:25.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:25.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:25.439][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:25.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:25.442][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.3*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:25.445][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:25.446][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:25.447][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.3%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:02:25.843][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.3%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:02:26.248][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:26.253][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f88afce5e7bcb0842d474b04c0bef37a.content" biodb.TRACE[2024-07-06 16:02:26.261][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f88afce5e7bcb0842d474b04c0bef37a.request" biodb.DEBUG[2024-07-06 16:02:26.267][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:26.269][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:26.271][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:26.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:26.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:26.284][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:26.286][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:26.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:26.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:26.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:26.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:26.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:26.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:26.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:26.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:26.302][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:26.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:26.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:26.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:26.309][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:26.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:26.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:26.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:26.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:26.319][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:26.320][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:26.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:26.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:26.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:26.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:26.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:26.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:26.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:26.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:26.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:26.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:26.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:26.333][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:26.334][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:26.335][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:26.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:26.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:26.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:26.342][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:26.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:26.344][private$loadEntries] Creating entries from ids [1]: "27495". biodb.DEBUG[2024-07-06 16:02:26.345][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:26.346][cch$loadFileContent] Trying to load 1 files from cache: [1]: "27495". biodb.TRACE[2024-07-06 16:02:26.347][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:26.348][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:26.349][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:26.350][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:26.358][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:26.359][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:26.362][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:26.363][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:26.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:26.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:26.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:26.369][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:26.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:26.371][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=27495". biodb.DEBUG[2024-07-06 16:02:26.373][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:26.374][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:26.375][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=27495". biodb.TRACE[2024-07-06 16:02:26.773][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=27495). biodb.DEBUG[2024-07-06 16:02:27.287][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:27.291][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/edda5d46cbbeda6cad9b4593b6925e01.content" biodb.TRACE[2024-07-06 16:02:27.298][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/edda5d46cbbeda6cad9b4593b6925e01.request" biodb.TRACE[2024-07-06 16:02:27.303][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/27495.xml" biodb.DEBUG[2024-07-06 16:02:27.306][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:27.308][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:27.311][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:27.314][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:27.316][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:27.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:27.327][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:27.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:27.331][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:27.332][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:27.336][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:27.338][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:27.340][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.341][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.343][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:27.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:27.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.349][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:27.351][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:27.352][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.353][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.355][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:27.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:27.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.360][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:27.361][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:27.362][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.363][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.365][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:27.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:27.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.369][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:27.370][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:27.371][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.372][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.373][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:27.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:27.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.377][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:27.378][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:27.379][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.380][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.381][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:27.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:27.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.385][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:27.385][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:27.386][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.387][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.388][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:27.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:27.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.392][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:27.393][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:27.394][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.394][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.395][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:27.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:27.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.399][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.400][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.401][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.402][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.403][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.406][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:27.407][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:27.408][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.409][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.410][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:27.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:27.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.412][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.413][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:27.414][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:27.415][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.416][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.417][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:27.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:27.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.421][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:27.422][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:27.422][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.423][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.424][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:27.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:27.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.427][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.434][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.435][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:27.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:27.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.442][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:27.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:27.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.446][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:27.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:27.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:27.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:27.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:27.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:27.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:27.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:27.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:27.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:27.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:27.471][self$createEntryFromContent] Accession numbers: 27495. biodb.TRACE[2024-07-06 16:02:27.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.475][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.476][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:27.483][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:27.484][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:27.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:27.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:27.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:27.490][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:27.491][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:27.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:27.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.500][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:27.501][private$selectFields] biodb.TRACE[2024-07-06 16:02:27.502][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:27.503][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:27.503][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:27.504][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.505][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.506][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.507][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.508][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.509][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.510][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.510][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.511][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:27.512][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:27.513][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.514][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.515][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.515][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.516][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:27.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.528][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-07-06 16:02:27.529][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:27.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:27.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:27.534][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:27.535][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:27.536][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:27.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:27.538][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.545][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:27.546][private$selectFields] biodb.TRACE[2024-07-06 16:02:27.546][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:27.547][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:27.548][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:27.549][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.550][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.551][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.552][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.552][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.553][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.554][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.555][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.556][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:27.557][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:27.558][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.559][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.559][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.560][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.561][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:27.562][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.565][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.573][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [19804]. biodb.DEBUG[2024-07-06 16:02:27.574][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:27.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:27.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:27.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:27.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:27.581][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:27.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:27.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.586][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.586][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.589][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.590][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:27.591][private$selectFields] biodb.TRACE[2024-07-06 16:02:27.592][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:27.593][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:27.593][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:27.594][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.595][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.596][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.597][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.598][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.599][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.600][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.601][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.601][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:27.602][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:27.603][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.604][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.605][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.606][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.607][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:27.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:27.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.624][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [27495]. biodb.DEBUG[2024-07-06 16:02:27.625][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:27.625][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:02:27.627][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:27.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:27.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:27.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:27.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:27.634][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:27.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:27.638][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:27.640][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:27.642][cch$loadFileContent] Trying to load 1 files from cache: [1]: "acfa4b558978abf12409c2b56e678d03". biodb.TRACE[2024-07-06 16:02:27.643][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:27.644][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/acfa4b558978abf12409c2b56e678d03.content". biodb.DEBUG[2024-07-06 16:02:27.647][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:27.648][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:27.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:27.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:27.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:27.654][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:27.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:27.656][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:27.666][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:27.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:27.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:27.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:27.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:27.673][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:27.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:27.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.679][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.682][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:27.686][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:27.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:27.687][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:27.691][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:27.692][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:27.693][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:27.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:27.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.698][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:27.701][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:27.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:27.704][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:27.705][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:27.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:27.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:27.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:27.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:27.712][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:27.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:27.714][private$loadEntries] Creating entries from ids [1]: "65675". biodb.DEBUG[2024-07-06 16:02:27.715][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:27.716][cch$loadFileContent] Trying to load 1 files from cache: [1]: "65675". biodb.TRACE[2024-07-06 16:02:27.717][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:27.718][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:27.719][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:27.720][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:27.721][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:27.722][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:27.724][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:27.725][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:27.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:27.730][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:27.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:27.731][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:27.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:27.733][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65675". biodb.DEBUG[2024-07-06 16:02:27.736][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:27.737][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:27.738][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65675". biodb.TRACE[2024-07-06 16:02:28.147][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65675). biodb.DEBUG[2024-07-06 16:02:28.549][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:28.553][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5e9eb5601826c5f1539c216fc81b6e57.content" biodb.TRACE[2024-07-06 16:02:28.560][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5e9eb5601826c5f1539c216fc81b6e57.request" biodb.TRACE[2024-07-06 16:02:28.565][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65675.xml" biodb.DEBUG[2024-07-06 16:02:28.568][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:28.571][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:28.573][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:28.577][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:28.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:28.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:28.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:28.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:28.593][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:28.595][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:28.599][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:28.600][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:28.602][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.609][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.615][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:28.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:28.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.620][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:28.621][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:28.622][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.623][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.625][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:28.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:28.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.629][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:28.630][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:28.631][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.632][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.633][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:28.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:28.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.636][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.637][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:28.638][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:28.639][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.640][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.641][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:28.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:28.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.645][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:28.646][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:28.647][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.647][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.649][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:28.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:28.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.652][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:28.653][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:28.654][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.655][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.656][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:28.657][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:28.658][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.658][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.659][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:28.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:28.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.663][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:28.664][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:28.665][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.666][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.667][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:28.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:28.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.670][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:28.671][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:28.672][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.673][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.674][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:28.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:28.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.677][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:28.678][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:28.679][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.680][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.681][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:28.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:28.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.685][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:28.686][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:28.686][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.687][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.688][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:28.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:28.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:28.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:28.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:28.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:28.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.699][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:28.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:28.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:28.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:28.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:28.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:28.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:28.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:28.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:28.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:28.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.715][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.716][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:28.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:28.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:28.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:28.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:28.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:28.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:28.727][self$createEntryFromContent] Accession numbers: 65675. biodb.TRACE[2024-07-06 16:02:28.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:28.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:28.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.730][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:28.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:28.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:28.735][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:28.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:28.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:28.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:28.738][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:28.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:28.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:28.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:28.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:28.746][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:28.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:28.747][private$loadEntries] Creating entries from ids [1]: "66318". biodb.DEBUG[2024-07-06 16:02:28.748][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:28.750][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66318". biodb.TRACE[2024-07-06 16:02:28.751][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:28.752][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:28.753][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:28.754][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:28.755][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:28.756][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:28.758][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:28.759][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:28.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:28.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:28.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:28.765][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:28.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:28.771][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66318". biodb.DEBUG[2024-07-06 16:02:28.774][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:28.775][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:28.776][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66318". biodb.TRACE[2024-07-06 16:02:29.172][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66318). biodb.DEBUG[2024-07-06 16:02:29.611][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:29.615][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f7af403e0af2ad309d5e7b7572ad9eab.content" biodb.TRACE[2024-07-06 16:02:29.622][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f7af403e0af2ad309d5e7b7572ad9eab.request" biodb.TRACE[2024-07-06 16:02:29.627][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66318.xml" biodb.DEBUG[2024-07-06 16:02:29.630][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:29.632][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:29.635][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:29.638][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:29.640][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:29.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:29.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:29.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:29.655][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:29.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:29.660][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:29.662][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:29.664][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.665][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:29.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:29.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.671][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.673][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:29.675][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:29.676][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.677][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.679][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:29.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:29.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.684][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:29.685][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:29.686][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.687][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.688][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:29.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:29.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.692][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.693][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:29.694][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:29.695][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.696][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.697][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:29.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:29.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.701][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:29.702][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:29.703][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.703][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.705][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:29.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:29.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.708][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:29.709][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:29.710][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.711][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.712][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:29.713][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:29.714][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.714][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.715][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:29.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:29.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.718][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.719][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:29.720][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:29.721][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.722][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:29.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:29.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.726][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:29.727][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:29.728][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.729][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.730][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:29.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:29.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.733][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:29.734][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:29.735][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.736][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.737][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:29.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:29.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.740][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.741][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:29.742][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:29.742][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.743][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.744][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:29.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:29.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:29.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:29.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:29.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:29.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.755][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:29.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:29.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:29.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:29.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.762][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:29.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:29.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:29.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:29.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:29.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:29.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:29.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:29.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:29.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:29.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:29.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:29.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:29.783][self$createEntryFromContent] Accession numbers: 66318. biodb.TRACE[2024-07-06 16:02:29.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:29.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:29.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:29.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:29.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:29.799][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:29.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:29.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:29.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:29.802][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:29.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:29.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:29.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:29.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:29.809][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:29.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:29.811][private$loadEntries] Creating entries from ids [1]: "67547". biodb.DEBUG[2024-07-06 16:02:29.812][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:29.814][cch$loadFileContent] Trying to load 1 files from cache: [1]: "67547". biodb.TRACE[2024-07-06 16:02:29.815][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:29.816][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:29.817][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:29.817][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:29.818][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:29.819][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:29.822][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:29.822][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:29.823][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:29.827][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:29.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:29.829][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:29.829][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:29.830][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67547". biodb.DEBUG[2024-07-06 16:02:29.833][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:29.834][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:29.835][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67547". biodb.TRACE[2024-07-06 16:02:30.247][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67547). biodb.DEBUG[2024-07-06 16:02:30.756][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:30.760][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5dcb6d289b29a3e5a91ef3f664ac8354.content" biodb.TRACE[2024-07-06 16:02:30.767][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5dcb6d289b29a3e5a91ef3f664ac8354.request" biodb.TRACE[2024-07-06 16:02:30.772][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/67547.xml" biodb.DEBUG[2024-07-06 16:02:30.775][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:30.777][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:30.780][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:30.783][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:30.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:30.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:30.796][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:30.798][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:30.799][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:30.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:30.805][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:30.807][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:30.808][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.810][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:30.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:30.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.818][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:30.819][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:30.820][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.822][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.823][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:30.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:30.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.828][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:30.829][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:30.830][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.832][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.833][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:30.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:30.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.837][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:30.838][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:30.839][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.840][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.842][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:30.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:30.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.846][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:30.847][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:30.847][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.848][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.849][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:30.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:30.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.853][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:30.854][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:30.855][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.856][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.857][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:30.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:30.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.860][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:30.861][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:30.862][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.863][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.864][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:30.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:30.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.867][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.868][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:30.869][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:30.869][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.870][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:30.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:30.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.875][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:30.876][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:30.877][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.878][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.879][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:30.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:30.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.881][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.882][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:30.883][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:30.884][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.885][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.886][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:30.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:30.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.890][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:30.891][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:30.891][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.892][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.893][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:30.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:30.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.896][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:30.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:30.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:30.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:30.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:30.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:30.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.915][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:30.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:30.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:30.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:30.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:30.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:30.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:30.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:30.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:30.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:30.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:30.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:30.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:30.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:30.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:30.940][self$createEntryFromContent] Accession numbers: 67547. biodb.TRACE[2024-07-06 16:02:30.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:30.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:30.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:30.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:30.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:30.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:30.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:30.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:30.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:30.951][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:30.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:30.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:30.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:30.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:30.958][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:30.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:30.960][private$loadEntries] Creating entries from ids [1]: "69550". biodb.DEBUG[2024-07-06 16:02:30.961][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:30.962][cch$loadFileContent] Trying to load 1 files from cache: [1]: "69550". biodb.TRACE[2024-07-06 16:02:30.963][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:30.964][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:30.965][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:30.966][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:30.967][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:30.968][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:30.970][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:30.971][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:30.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:30.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:30.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:30.977][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:30.978][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:30.979][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69550". biodb.DEBUG[2024-07-06 16:02:30.982][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:30.982][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:30.984][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69550". biodb.TRACE[2024-07-06 16:02:31.384][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69550). biodb.DEBUG[2024-07-06 16:02:31.781][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:31.783][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/05703421c7bf99b1d8473c1de6165168.content" biodb.TRACE[2024-07-06 16:02:31.786][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/05703421c7bf99b1d8473c1de6165168.request" biodb.TRACE[2024-07-06 16:02:31.788][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/69550.xml" biodb.DEBUG[2024-07-06 16:02:31.789][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:31.791][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:31.792][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:31.793][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:31.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:31.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:31.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:31.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:31.801][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:31.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:31.804][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:31.805][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:31.806][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.807][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:31.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:31.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.812][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:31.813][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:31.814][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.815][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.816][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:31.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:31.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.820][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:31.821][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:31.822][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.823][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.824][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:31.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:31.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.828][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:31.829][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:31.830][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.831][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.832][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:31.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:31.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.836][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:31.837][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:31.838][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.839][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.840][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:31.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:31.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.843][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:31.844][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:31.845][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.846][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.847][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:31.848][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:31.849][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.850][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.851][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:31.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:31.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.854][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:31.855][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:31.860][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.864][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:31.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:31.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.869][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:31.870][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:31.871][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.872][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.873][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:31.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:31.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.876][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.876][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:31.877][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:31.878][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.879][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.880][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:31.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:31.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.884][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:31.885][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:31.885][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.886][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.887][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:31.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:31.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:31.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:31.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.893][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:31.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:31.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:31.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:31.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:31.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:31.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.905][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:31.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:31.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.908][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:31.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:31.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.912][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:31.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:31.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:31.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:31.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.919][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:31.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:31.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:31.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:31.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:31.925][self$createEntryFromContent] Accession numbers: 69550. biodb.TRACE[2024-07-06 16:02:31.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:31.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:31.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:31.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:31.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:31.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:31.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:31.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:31.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:31.937][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:31.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:31.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:31.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:31.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:31.944][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:31.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:31.946][private$loadEntries] Creating entries from ids [1]: "71520". biodb.DEBUG[2024-07-06 16:02:31.946][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:31.948][cch$loadFileContent] Trying to load 1 files from cache: [1]: "71520". biodb.TRACE[2024-07-06 16:02:31.949][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:31.950][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:31.951][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:31.952][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:31.953][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:31.953][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:31.956][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:31.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:31.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:31.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:31.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:31.963][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:31.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:31.965][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=71520". biodb.DEBUG[2024-07-06 16:02:31.967][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:31.968][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:31.969][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=71520". biodb.TRACE[2024-07-06 16:02:32.377][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=71520). biodb.DEBUG[2024-07-06 16:02:32.810][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:32.814][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e7ceab0ba86590faa4ea87df2e390610.content" biodb.TRACE[2024-07-06 16:02:32.821][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e7ceab0ba86590faa4ea87df2e390610.request" biodb.TRACE[2024-07-06 16:02:32.826][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/71520.xml" biodb.DEBUG[2024-07-06 16:02:32.829][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:32.832][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:32.834][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:32.838][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:32.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:32.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:32.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:32.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:32.854][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:32.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:32.860][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:32.861][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:32.863][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.864][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:32.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:32.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.872][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:32.873][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:32.875][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.876][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.878][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:32.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:32.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.881][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.883][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:32.884][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:32.892][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.894][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.895][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:32.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:32.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.899][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:32.900][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:32.901][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.902][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.903][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:32.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:32.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.907][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:32.908][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:32.908][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.909][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:32.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:32.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.914][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:32.915][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:32.916][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.916][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.917][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:32.918][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:32.919][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.920][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.921][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:32.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:32.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.924][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.925][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:32.926][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:32.926][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.927][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:32.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:32.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.932][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:32.933][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:32.934][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.934][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.936][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:32.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:32.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.939][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:32.940][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:32.941][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.942][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.943][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:32.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:32.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.945][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.946][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:32.947][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:32.948][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.949][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.950][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:32.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:32.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:32.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:32.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:32.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:32.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:32.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:32.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.963][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.964][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:32.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:32.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:32.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:32.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.971][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:32.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:32.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.974][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:32.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:32.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.977][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.978][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:32.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:32.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:32.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:32.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.984][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.985][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:32.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:32.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:32.988][self$createEntryFromContent] Accession numbers: 71520. biodb.TRACE[2024-07-06 16:02:32.989][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:32.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:32.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:32.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:32.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:32.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:32.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:32.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:32.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:33.000][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:33.000][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:33.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:33.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:33.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:33.007][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:33.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:33.009][private$loadEntries] Creating entries from ids [1]: "77600". biodb.DEBUG[2024-07-06 16:02:33.009][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:33.011][cch$loadFileContent] Trying to load 1 files from cache: [1]: "77600". biodb.TRACE[2024-07-06 16:02:33.012][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:33.013][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:33.014][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:33.015][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:33.016][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:33.017][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:33.019][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:33.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:33.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:33.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:33.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:33.026][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:33.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:33.028][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77600". biodb.DEBUG[2024-07-06 16:02:33.031][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:33.031][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:33.033][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77600". biodb.TRACE[2024-07-06 16:02:33.426][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77600). biodb.DEBUG[2024-07-06 16:02:33.998][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:34.000][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/91aa415bb91d90afd912e94b5d252faa.content" biodb.TRACE[2024-07-06 16:02:34.011][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/91aa415bb91d90afd912e94b5d252faa.request" biodb.TRACE[2024-07-06 16:02:34.013][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/77600.xml" biodb.DEBUG[2024-07-06 16:02:34.014][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:34.016][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:34.017][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:34.018][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:34.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:34.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:34.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:34.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:34.025][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:34.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:34.029][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:34.030][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:34.030][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.031][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:34.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:34.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.036][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:34.037][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:34.038][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.039][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.040][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:34.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:34.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.044][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:34.045][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:34.045][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.046][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.047][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:34.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:34.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.051][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:34.052][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:34.053][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.054][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:34.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:34.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.058][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:34.059][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:34.060][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.061][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.062][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:34.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:34.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.066][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:34.067][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:34.067][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.068][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.069][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:34.070][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:34.071][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.072][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.073][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:34.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:34.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.077][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:34.077][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:34.078][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.079][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:34.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:34.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.084][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:34.085][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:34.085][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.086][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:34.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:34.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.091][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:34.092][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:34.093][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.094][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.095][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:34.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:34.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.098][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:34.099][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:34.100][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.101][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.102][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:34.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:34.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:34.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:34.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:34.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:34.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:34.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:34.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:34.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:34.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:34.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:34.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:34.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:34.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:34.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:34.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:34.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:34.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:34.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:34.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:34.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:34.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:34.141][self$createEntryFromContent] Accession numbers: 77600. biodb.TRACE[2024-07-06 16:02:34.142][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:34.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:34.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.146][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:34.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:34.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:34.149][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:34.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:34.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:34.152][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:34.153][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:34.154][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:34.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:34.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:34.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:34.165][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:34.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:34.167][private$loadEntries] Creating entries from ids [1]: "77601". biodb.DEBUG[2024-07-06 16:02:34.168][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:34.169][cch$loadFileContent] Trying to load 1 files from cache: [1]: "77601". biodb.TRACE[2024-07-06 16:02:34.170][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:34.171][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:34.172][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:34.173][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:34.174][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:34.175][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:34.178][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:34.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:34.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:34.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:34.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:34.185][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:34.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:34.187][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77601". biodb.DEBUG[2024-07-06 16:02:34.189][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:34.190][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:34.191][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77601". biodb.TRACE[2024-07-06 16:02:34.603][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77601). biodb.DEBUG[2024-07-06 16:02:35.046][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:35.051][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ff0e48db0e5117b4127b12d15d1485a8.content" biodb.TRACE[2024-07-06 16:02:35.057][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ff0e48db0e5117b4127b12d15d1485a8.request" biodb.TRACE[2024-07-06 16:02:35.063][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/77601.xml" biodb.DEBUG[2024-07-06 16:02:35.066][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:35.068][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:35.071][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:35.074][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.090][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.096][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:35.098][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:35.099][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.101][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:35.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:35.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.109][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:35.110][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:35.111][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.113][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.114][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:35.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:35.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.119][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:35.120][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:35.121][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.122][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.124][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:35.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:35.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.128][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:35.129][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:35.130][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.131][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.132][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:35.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:35.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.136][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:35.137][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:35.138][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.139][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.140][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:35.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:35.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.144][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:35.145][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:35.146][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.146][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.147][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:35.148][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.149][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.150][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.151][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:35.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.155][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:35.156][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:35.156][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.157][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.158][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:35.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:35.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.162][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:35.163][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:35.164][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.165][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.166][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:35.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:35.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.169][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:35.170][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:35.171][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.172][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.173][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:35.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:35.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.177][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:35.178][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:35.178][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.179][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.180][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:35.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:35.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.191][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:35.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:35.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:35.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:35.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:35.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:35.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:35.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:35.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:35.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:35.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.220][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:35.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:35.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:35.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:35.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:35.227][self$createEntryFromContent] Accession numbers: 77601. biodb.TRACE[2024-07-06 16:02:35.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:35.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:35.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:35.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:35.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:35.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:35.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:35.238][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:35.240][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.241][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.245][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.247][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.252][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.256][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.257][private$selectFields] biodb.TRACE[2024-07-06 16:02:35.257][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:35.258][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:35.259][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.260][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.261][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.262][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.263][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.263][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.264][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.265][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.266][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.267][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.268][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.269][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.269][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.270][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.271][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.272][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:35.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.284][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [64199]. biodb.DEBUG[2024-07-06 16:02:35.285][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.285][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.290][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.292][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.297][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.300][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.301][private$selectFields] biodb.TRACE[2024-07-06 16:02:35.302][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:35.303][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:35.304][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.305][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.306][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.307][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.307][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.308][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.309][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.310][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.311][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.312][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.313][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.313][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.314][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.315][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.316][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.317][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:35.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.327][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.329][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [77600]. biodb.DEBUG[2024-07-06 16:02:35.330][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.330][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.335][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.336][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.337][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.339][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.346][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.347][private$selectFields] biodb.TRACE[2024-07-06 16:02:35.347][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:35.348][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:35.349][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.350][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.351][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.352][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.353][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.353][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.354][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.355][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.366][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.367][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.368][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.368][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.369][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.370][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.371][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.372][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:35.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.376][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.384][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [77601]. biodb.DEBUG[2024-07-06 16:02:35.384][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:35.385][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-07-06 16:02:35.392][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-07-06 16:02:35.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-07-06 16:02:35.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.396][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-07-06 16:02:35.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-07-06 16:02:35.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.399][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-07-06 16:02:35.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-07-06 16:02:35.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-07-06 16:02:35.405][biodb::testThat] biodb.INFO [2024-07-06 16:02:35.406][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() "). biodb.INFO [2024-07-06 16:02:35.407][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-07-06 16:02:35.408][biodb::testThat] biodb.TRACE[2024-07-06 16:02:35.410][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-07-06 16:02:35.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-07-06 16:02:35.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.414][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-07-06 16:02:35.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-07-06 16:02:35.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.416][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.417][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-07-06 16:02:35.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-07-06 16:02:35.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.424][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.427][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.428][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.431][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.434][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.437][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.441][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.452][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.455][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.456][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.462][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:35.466][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.471][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.473][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:35.476][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:35.479][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:35.480][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-07-06 16:02:35.481][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:35.482][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-07-06 16:02:35.484][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.485][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.491][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.493][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.497][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:35.505][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:35.508][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:35.509][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-07-06 16:02:35.510][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:35.511][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-07-06 16:02:35.513][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.525][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.534][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:35.537][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.538][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.539][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.543][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.544][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.544][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.546][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:35.557][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:35.558][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.559][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.560][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.565][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.574][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.574][private$selectFields] biodb.TRACE[2024-07-06 16:02:35.575][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:35.576][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:35.577][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.578][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.579][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.580][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.580][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.581][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.582][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.583][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.584][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.585][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.586][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.586][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.587][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.588][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.589][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.590][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:35.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.602][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288]. biodb.DEBUG[2024-07-06 16:02:35.603][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.608][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.609][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.610][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.610][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.618][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.619][private$selectFields] biodb.TRACE[2024-07-06 16:02:35.620][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:35.621][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:35.622][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.623][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.624][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.624][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.625][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.626][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.627][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.628][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.629][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.630][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.630][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.631][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.632][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.633][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.634][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.635][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:35.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.639][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.642][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.647][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-07-06 16:02:35.648][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.655][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.663][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.664][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.665][private$selectFields] biodb.TRACE[2024-07-06 16:02:35.670][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:35.671][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:35.672][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.673][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.674][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.675][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.676][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.677][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.678][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.679][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.679][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.680][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.681][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.682][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.683][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.684][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.685][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.685][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:35.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.692][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.697][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892]. biodb.DEBUG[2024-07-06 16:02:35.698][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:35.699][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:02:35.701][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.706][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.708][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:35.711][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:35.714][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:35.715][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b3cd8ddf08f509014f10dc9bf7c1649d". biodb.TRACE[2024-07-06 16:02:35.716][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:35.717][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b3cd8ddf08f509014f10dc9bf7c1649d.content". biodb.DEBUG[2024-07-06 16:02:35.719][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.724][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.726][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.728][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.730][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.731][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:35.738][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.745][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.747][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.751][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:35.758][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:35.761][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:35.762][cch$loadFileContent] Trying to load 1 files from cache: [1]: "831507e33c6cf42061851262412f5feb". biodb.TRACE[2024-07-06 16:02:35.763][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:35.764][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/831507e33c6cf42061851262412f5feb.content". biodb.DEBUG[2024-07-06 16:02:35.767][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.768][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.774][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.776][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.779][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.783][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:35.786][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.794][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.795][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.799][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:35.806][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.808][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.812][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.813][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:35.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:35.831][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:35.833][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.838][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.840][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.848][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.849][private$selectFields] biodb.TRACE[2024-07-06 16:02:35.850][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:35.851][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:35.852][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.853][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.854][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.855][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.855][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.856][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.857][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.858][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.859][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.860][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.861][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.861][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.862][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.863][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.864][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.865][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:35.866][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.877][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-07-06 16:02:35.877][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.878][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.879][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.883][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.885][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.885][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.893][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.894][private$selectFields] biodb.TRACE[2024-07-06 16:02:35.895][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:35.896][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:35.897][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.897][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.898][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.899][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.900][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.901][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.902][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.903][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.904][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.904][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.905][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.906][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.907][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.908][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.909][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.910][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:35.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.921][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-07-06 16:02:35.922][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.928][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.929][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:35.931][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.938][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.939][private$selectFields] biodb.TRACE[2024-07-06 16:02:35.940][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:35.941][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:35.942][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.943][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.943][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.944][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.945][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.946][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.947][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.948][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.949][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.950][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.951][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:35.951][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.952][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.953][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.954][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.955][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:35.956][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.963][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:35.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:35.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:35.967][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [19804]. biodb.DEBUG[2024-07-06 16:02:35.968][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:35.969][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:02:35.975][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.981][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:35.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:35.982][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:35.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:35.985][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:35.988][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:35.989][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26d0872875c47c33e8205aa7124e0486". biodb.TRACE[2024-07-06 16:02:35.990][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:35.992][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26d0872875c47c33e8205aa7124e0486.content". biodb.DEBUG[2024-07-06 16:02:35.994][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:35.995][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:35.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:35.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.001][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.003][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.006][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.010][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.013][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.019][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.020][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.025][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.029][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.032][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.039][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.052][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.059][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.061][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.064][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.068][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.071][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.078][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.079][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.087][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.091][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.098][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.107][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.110][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.117][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.131][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.134][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.141][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.143][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.146][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.150][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.154][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:36.157][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:36.158][cch$loadFileContent] Trying to load 1 files from cache: [1]: "357534c211a0779cb44e196fcebae6c0". biodb.TRACE[2024-07-06 16:02:36.159][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:36.160][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/357534c211a0779cb44e196fcebae6c0.content". biodb.DEBUG[2024-07-06 16:02:36.162][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.163][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.169][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.174][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.178][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.181][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.188][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.200][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.202][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.207][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:36.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.219][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:36.221][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.222][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.226][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.228][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.236][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.237][private$selectFields] biodb.TRACE[2024-07-06 16:02:36.238][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:36.239][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:36.240][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.241][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.242][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.242][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.243][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.244][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.245][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.246][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.247][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.248][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.249][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.250][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.250][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.251][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.252][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.253][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:36.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.261][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.265][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-07-06 16:02:36.266][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.267][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.267][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.271][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.277][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.280][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.287][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.288][private$selectFields] biodb.TRACE[2024-07-06 16:02:36.289][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:36.289][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:36.290][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.291][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.292][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.293][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.294][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.294][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.295][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.296][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.297][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.298][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.299][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.300][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.301][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.301][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.302][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.303][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:36.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.315][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [71954]. biodb.DEBUG[2024-07-06 16:02:36.316][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.323][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.327][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.328][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.332][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.333][private$selectFields] biodb.TRACE[2024-07-06 16:02:36.333][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:36.334][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:36.335][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.336][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.337][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.338][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.338][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.339][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.340][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.341][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.342][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.343][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.344][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.344][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.345][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.346][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.347][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.348][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:36.349][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.352][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.359][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [197612]. biodb.DEBUG[2024-07-06 16:02:36.360][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:36.361][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-07-06 16:02:36.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.387][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.390][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.394][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.400][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.407][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.422][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.427][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.428][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.432][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.433][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.434][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.435][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:36.437][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:36.440][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:36.441][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2024-07-06 16:02:36.442][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:36.443][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2024-07-06 16:02:36.446][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:36.449][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:36.450][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2024-07-06 16:02:36.451][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:36.452][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2024-07-06 16:02:36.454][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.461][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.463][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.470][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.473][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.480][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.482][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.488][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.489][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.491][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.492][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.498][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.499][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.511][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:36.513][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.514][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.520][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.528][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.529][private$selectFields] biodb.TRACE[2024-07-06 16:02:36.530][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:36.531][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:36.532][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.533][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.533][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.534][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.535][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.536][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.537][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.538][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.539][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.539][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.540][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.541][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.542][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.543][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.544][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.545][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:36.546][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.549][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.553][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.557][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2024-07-06 16:02:36.558][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.558][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.559][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.563][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.564][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.565][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.595][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.597][private$selectFields] biodb.TRACE[2024-07-06 16:02:36.598][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:36.599][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:36.600][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.602][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.603][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.604][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.605][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.606][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.607][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.607][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.608][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.609][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.610][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.611][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.612][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.613][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.614][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.615][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:36.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.620][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.626][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.628][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-07-06 16:02:36.629][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.630][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.635][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.636][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.637][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.639][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.642][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.647][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.647][private$selectFields] biodb.TRACE[2024-07-06 16:02:36.648][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:36.649][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:36.650][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.651][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.652][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.653][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.654][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.655][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.656][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.657][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.658][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.659][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.659][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.660][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.661][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.662][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.663][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.664][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:36.665][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.673][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.675][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.677][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2024-07-06 16:02:36.677][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:36.678][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:02:36.680][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.688][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:36.692][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.29*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:36.695][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:36.696][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7269bbea581f1e243800f8ee4e0f4fdb". biodb.TRACE[2024-07-06 16:02:36.697][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:36.699][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7269bbea581f1e243800f8ee4e0f4fdb.content". biodb.DEBUG[2024-07-06 16:02:36.701][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.709][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.722][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.723][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.724][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.728][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.730][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.739][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.743][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.751][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.761][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.765][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.768][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:36.770][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.771][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.771][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.777][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.782][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.786][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.787][private$selectFields] biodb.TRACE[2024-07-06 16:02:36.787][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:36.788][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:36.789][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.790][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.791][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.792][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.793][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.793][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.794][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.795][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.796][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.797][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.798][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.799][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.800][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.800][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.801][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.802][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:36.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.806][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.814][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-07-06 16:02:36.815][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.822][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.827][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.831][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.831][private$selectFields] biodb.TRACE[2024-07-06 16:02:36.832][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:36.833][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:36.834][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.835][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.836][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.837][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.837][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.838][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.839][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.840][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.841][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.842][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.843][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.843][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.844][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.845][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.846][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.847][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:36.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.855][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.859][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [91601]. biodb.DEBUG[2024-07-06 16:02:36.860][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.867][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.876][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.877][private$selectFields] biodb.TRACE[2024-07-06 16:02:36.878][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:36.878][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:36.879][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.880][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.881][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.882][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.883][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.884][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.885][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.886][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.886][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.887][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.888][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:36.889][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.890][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.891][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.892][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.893][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:36.894][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.896][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.901][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:36.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.905][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [95147]. biodb.DEBUG[2024-07-06 16:02:36.906][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:36.911][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:02:36.913][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.915][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.921][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:36.924][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:36.926][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:36.928][cch$loadFileContent] Trying to load 1 files from cache: [1]: "acfa4b558978abf12409c2b56e678d03". biodb.TRACE[2024-07-06 16:02:36.929][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:36.930][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/acfa4b558978abf12409c2b56e678d03.content". biodb.DEBUG[2024-07-06 16:02:36.932][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.939][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.948][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.952][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.952][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.953][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.957][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.959][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.959][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.960][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.963][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.971][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.972][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.973][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.976][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.978][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:36.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:36.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:36.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:36.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:36.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:36.991][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:36.992][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:36.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:36.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:36.997][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:36.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:36.999][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:37.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:37.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.004][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.008][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:37.009][private$selectFields] biodb.TRACE[2024-07-06 16:02:37.010][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:37.010][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:37.011][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:37.012][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.013][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.014][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.015][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.016][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.017][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.017][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.018][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.019][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:37.020][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:37.021][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.022][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.023][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.024][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.024][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:37.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.033][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.036][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [636]. biodb.DEBUG[2024-07-06 16:02:37.037][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:37.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:37.039][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:37.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:37.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:37.045][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:37.046][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:37.047][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.054][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:37.055][private$selectFields] biodb.TRACE[2024-07-06 16:02:37.056][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:37.056][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:37.057][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:37.058][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.064][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.065][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.066][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.067][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.068][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.069][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.070][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.070][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:37.071][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:37.072][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.073][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.074][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.075][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.076][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:37.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.087][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [64199]. biodb.DEBUG[2024-07-06 16:02:37.088][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:37.089][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:37.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:37.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:37.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:37.096][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:37.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:37.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.101][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.105][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:37.105][private$selectFields] biodb.TRACE[2024-07-06 16:02:37.106][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:37.107][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:37.108][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:37.109][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.110][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.111][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.111][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.112][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.113][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.114][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.115][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.116][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:37.117][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:37.118][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.118][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.119][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.120][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.121][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:37.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.125][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:37.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.133][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [65648]. biodb.DEBUG[2024-07-06 16:02:37.134][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:37.134][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-07-06 16:02:37.150][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-07-06 16:02:37.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-07-06 16:02:37.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.154][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-07-06 16:02:37.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-07-06 16:02:37.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.157][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-07-06 16:02:37.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-07-06 16:02:37.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.163][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:37.163][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:37.164][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.165][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.166][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:37.167][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:37.168][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.169][ef$get] fields variable is a list. biodb.INFO [2024-07-06 16:02:37.170][biodb::testThat] biodb.INFO [2024-07-06 16:02:37.171][biodb::testThat] Running test function test.annotateMzValues_real_values (" annotateMzValues() works correctly with real values. "). biodb.INFO [2024-07-06 16:02:37.172][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-07-06 16:02:37.173][biodb::testThat] biodb.TRACE[2024-07-06 16:02:37.175][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-07-06 16:02:37.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-07-06 16:02:37.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.179][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-07-06 16:02:37.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-07-06 16:02:37.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.182][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-07-06 16:02:37.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-07-06 16:02:37.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.197][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.200][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.203][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.204][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.208][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.220][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.227][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:37.230][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:37.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:37.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:37.236][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:37.236][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:37.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:37.241][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:37.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:37.243][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:37.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:37.246][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.5*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:37.249][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:37.250][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:37.251][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.5%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:02:37.652][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.5%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:02:38.315][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:38.319][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ebf8c17fa19fb0caf99d83ca8441a2ac.content" biodb.TRACE[2024-07-06 16:02:38.327][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ebf8c17fa19fb0caf99d83ca8441a2ac.request" biodb.DEBUG[2024-07-06 16:02:38.338][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:38.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:38.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:38.351][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:38.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:38.355][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:38.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:38.359][private$loadEntries] Creating entries from ids [1]: "3014". biodb.DEBUG[2024-07-06 16:02:38.360][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:38.363][cch$loadFileContent] Trying to load 1 files from cache: [1]: "3014". biodb.TRACE[2024-07-06 16:02:38.365][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:38.367][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:38.369][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:38.370][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:38.372][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:38.373][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:38.377][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:38.378][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:38.379][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:38.385][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:38.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:38.387][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:38.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:38.389][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3014". biodb.DEBUG[2024-07-06 16:02:38.392][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:38.393][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:38.395][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3014". biodb.TRACE[2024-07-06 16:02:38.786][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=3014). biodb.DEBUG[2024-07-06 16:02:39.217][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:39.221][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/48c0bb0df5de824dbe83babbff8d81fe.content" biodb.TRACE[2024-07-06 16:02:39.228][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/48c0bb0df5de824dbe83babbff8d81fe.request" biodb.TRACE[2024-07-06 16:02:39.233][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/3014.xml" biodb.DEBUG[2024-07-06 16:02:39.236][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:39.238][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:39.241][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:39.244][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:39.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:39.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:39.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:39.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:39.261][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:39.262][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:39.266][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:39.268][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:39.269][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.271][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:39.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:39.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.279][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:39.280][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:39.281][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.283][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.284][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:39.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:39.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.290][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:39.291][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:39.292][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.293][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.295][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:39.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:39.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.299][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:39.300][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:39.301][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.302][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.303][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:39.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:39.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.307][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:39.308][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:39.309][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.310][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.311][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:39.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:39.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.315][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:39.316][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:39.317][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.317][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.319][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:39.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:39.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.332][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:39.333][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:39.334][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.335][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.336][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:39.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:39.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.340][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:39.341][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:39.342][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.342][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.343][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:39.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:39.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.347][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:39.348][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:39.349][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.350][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.351][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:39.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:39.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.354][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:39.355][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:39.356][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.357][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.358][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:39.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:39.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.362][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:39.363][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:39.363][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.364][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.365][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:39.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:39.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:39.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:39.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:39.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:39.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:39.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:39.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:39.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:39.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:39.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:39.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:39.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:39.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.389][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:39.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:39.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:39.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:39.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:39.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:39.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.400][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:39.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:39.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:39.404][self$createEntryFromContent] Accession numbers: 3014. biodb.TRACE[2024-07-06 16:02:39.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:39.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:39.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.407][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.408][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:39.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:39.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:39.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:39.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:39.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:39.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:39.415][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:39.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:39.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:39.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:39.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:39.422][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:39.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:39.424][private$loadEntries] Creating entries from ids [1]: "7567". biodb.DEBUG[2024-07-06 16:02:39.425][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:39.427][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7567". biodb.TRACE[2024-07-06 16:02:39.428][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:39.429][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:39.430][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:39.431][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:39.431][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:39.432][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:39.435][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:39.435][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:39.436][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:39.440][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:39.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:39.442][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:39.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:39.444][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7567". biodb.DEBUG[2024-07-06 16:02:39.446][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:39.447][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:39.448][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7567". biodb.TRACE[2024-07-06 16:02:39.849][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7567). biodb.DEBUG[2024-07-06 16:02:40.276][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:40.280][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d5365299c16307afdd0b9fe7b73b123c.content" biodb.TRACE[2024-07-06 16:02:40.287][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d5365299c16307afdd0b9fe7b73b123c.request" biodb.TRACE[2024-07-06 16:02:40.292][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7567.xml" biodb.DEBUG[2024-07-06 16:02:40.295][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:40.298][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:40.300][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:40.304][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:40.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:40.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:40.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:40.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:40.320][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:40.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:40.326][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:40.327][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:40.329][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.340][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.342][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:40.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:40.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.347][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:40.349][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:40.350][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.351][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.352][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:40.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:40.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.357][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:40.358][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:40.359][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.360][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.361][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:40.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:40.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.364][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.365][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:40.366][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:40.367][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.368][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.369][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:40.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:40.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.372][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:40.373][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:40.374][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.375][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.376][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:40.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:40.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.380][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:40.381][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:40.381][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.382][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.383][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:40.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:40.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.387][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:40.388][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:40.389][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.390][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.391][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:40.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:40.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.394][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:40.395][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:40.396][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.397][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:40.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:40.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.400][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.401][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:40.402][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:40.403][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.404][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.405][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:40.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:40.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.409][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:40.410][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:40.410][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.411][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.412][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:40.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:40.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.416][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:40.417][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:40.418][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.418][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.419][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:40.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:40.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.423][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:40.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:40.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.427][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:40.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:40.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:40.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:40.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:40.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:40.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.437][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:40.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:40.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:40.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:40.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:40.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:40.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:40.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:40.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:40.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:40.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.455][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:40.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:40.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.457][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:40.458][self$createEntryFromContent] Accession numbers: 7567. biodb.TRACE[2024-07-06 16:02:40.459][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:40.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:40.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.462][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:40.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:40.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:40.466][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:40.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:40.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:40.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:40.470][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:40.471][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:40.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:40.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:40.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:40.477][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:40.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:40.479][private$loadEntries] Creating entries from ids [1]: "8021". biodb.DEBUG[2024-07-06 16:02:40.480][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:40.481][cch$loadFileContent] Trying to load 1 files from cache: [1]: "8021". biodb.TRACE[2024-07-06 16:02:40.482][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:40.483][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:40.484][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:40.485][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:40.486][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:40.487][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:40.489][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:40.490][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:40.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:40.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:40.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:40.501][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:40.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:40.503][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=8021". biodb.DEBUG[2024-07-06 16:02:40.506][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:40.507][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:40.508][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=8021". biodb.TRACE[2024-07-06 16:02:40.898][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=8021). biodb.DEBUG[2024-07-06 16:02:41.316][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:41.320][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6017fc384c334739eec9b216fa851a5.content" biodb.TRACE[2024-07-06 16:02:41.327][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6017fc384c334739eec9b216fa851a5.request" biodb.TRACE[2024-07-06 16:02:41.333][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8021.xml" biodb.DEBUG[2024-07-06 16:02:41.335][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:41.338][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:41.341][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:41.344][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:41.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:41.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:41.357][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:41.358][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:41.360][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:41.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:41.366][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:41.368][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:41.369][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.371][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:41.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:41.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.379][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:41.380][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:41.381][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.383][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.384][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:41.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:41.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.389][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:41.390][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:41.391][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.392][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.394][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:41.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:41.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.398][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:41.399][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:41.400][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.401][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.402][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:41.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:41.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.406][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:41.407][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:41.408][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.409][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:41.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:41.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.414][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:41.415][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:41.415][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.416][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.417][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:41.418][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:41.419][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.420][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.421][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:41.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:41.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.425][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:41.426][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:41.426][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.427][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:41.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:41.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.432][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:41.433][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:41.434][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.434][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.436][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:41.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:41.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.439][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:41.440][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:41.441][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.442][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.443][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:41.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:41.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.446][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:41.447][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:41.448][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.449][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.450][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:41.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:41.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.454][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:41.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:41.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:41.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:41.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:41.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:41.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.464][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:41.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:41.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.468][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:41.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:41.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.472][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:41.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:41.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:41.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:41.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:41.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:41.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.481][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:41.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:41.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.486][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:41.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:41.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:41.497][self$createEntryFromContent] Accession numbers: 8021. biodb.TRACE[2024-07-06 16:02:41.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:41.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:41.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:41.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:41.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:41.505][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:41.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:41.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:41.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:41.509][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:41.510][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:41.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:41.514][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:41.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:41.516][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:41.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:41.518][private$loadEntries] Creating entries from ids [1]: "30382". biodb.DEBUG[2024-07-06 16:02:41.519][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:41.520][cch$loadFileContent] Trying to load 1 files from cache: [1]: "30382". biodb.TRACE[2024-07-06 16:02:41.521][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:41.522][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:41.523][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:41.524][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:41.525][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:41.526][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:41.528][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:41.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:41.530][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:41.533][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:41.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:41.535][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:41.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:41.537][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=30382". biodb.DEBUG[2024-07-06 16:02:41.539][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:41.540][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:41.541][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=30382". biodb.TRACE[2024-07-06 16:02:41.934][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=30382). biodb.DEBUG[2024-07-06 16:02:42.367][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:42.371][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/762ae1b4688e0a5ef1a1419b25f545f9.content" biodb.TRACE[2024-07-06 16:02:42.378][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/762ae1b4688e0a5ef1a1419b25f545f9.request" biodb.TRACE[2024-07-06 16:02:42.383][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/30382.xml" biodb.DEBUG[2024-07-06 16:02:42.386][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:42.389][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:42.391][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:42.394][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:42.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:42.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:42.407][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:42.409][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:42.411][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:42.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:42.416][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:42.418][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:42.420][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.421][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:42.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:42.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.429][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:42.431][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:42.432][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.433][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.435][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:42.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:42.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.440][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:42.441][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:42.442][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.443][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.445][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:42.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:42.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.449][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:42.450][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:42.451][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.452][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.453][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:42.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:42.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.457][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:42.458][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:42.459][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.460][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.461][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:42.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:42.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.465][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:42.465][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:42.466][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.467][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.468][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:42.469][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:42.470][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.471][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.472][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:42.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:42.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.475][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.476][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:42.477][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:42.477][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.478][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.479][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:42.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:42.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.483][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:42.484][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:42.485][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.486][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.487][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:42.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:42.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.491][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:42.492][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:42.492][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.493][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.494][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:42.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:42.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.498][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:42.499][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:42.500][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.500][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.502][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:42.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:42.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.513][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.520][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:42.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:42.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:42.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:42.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:42.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:42.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.534][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:42.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:42.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:42.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:42.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.541][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:42.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:42.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:42.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:42.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:42.548][self$createEntryFromContent] Accession numbers: 30382. biodb.TRACE[2024-07-06 16:02:42.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:42.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:42.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.553][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:42.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:42.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:42.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:42.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:42.560][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:42.561][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:42.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:42.563][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:42.567][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:42.568][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:42.569][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:42.569][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:42.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.577][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:42.578][private$selectFields] biodb.TRACE[2024-07-06 16:02:42.579][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:42.580][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:42.581][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:42.582][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.582][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.583][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.584][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.585][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.586][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.587][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.588][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.589][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:42.589][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:42.590][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.591][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.592][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.593][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.594][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:42.595][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.598][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.602][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.605][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [3014]. biodb.DEBUG[2024-07-06 16:02:42.606][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:42.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:42.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:42.612][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:42.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:42.613][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:42.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:42.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.622][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:42.623][private$selectFields] biodb.TRACE[2024-07-06 16:02:42.624][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:42.625][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:42.626][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:42.627][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.628][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.629][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.629][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.630][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.631][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.632][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.633][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.634][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:42.635][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:42.636][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.637][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.637][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.638][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.639][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:42.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.643][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.650][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.651][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [8021]. biodb.DEBUG[2024-07-06 16:02:42.652][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:42.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:42.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:42.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:42.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:42.664][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:42.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:42.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.673][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:42.674][private$selectFields] biodb.TRACE[2024-07-06 16:02:42.675][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:42.676][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:42.676][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:42.677][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.678][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.679][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.680][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.681][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.682][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.683][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.683][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.684][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:42.685][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:42.686][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.687][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.688][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.689][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.690][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:42.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.693][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.697][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:42.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:42.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:42.701][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [30382]. biodb.DEBUG[2024-07-06 16:02:42.702][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:42.703][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:02:42.705][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:42.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:42.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:42.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:42.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:42.712][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:42.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:42.715][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.4*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:42.718][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:42.719][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:42.721][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.4%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:02:43.114][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.4%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:02:43.547][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:43.550][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/152225e020c3e5947a0f5a90f021cee7.content" biodb.TRACE[2024-07-06 16:02:43.556][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/152225e020c3e5947a0f5a90f021cee7.request" biodb.DEBUG[2024-07-06 16:02:43.562][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:43.563][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:43.565][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:43.572][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:43.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:43.575][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:43.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:43.578][private$loadEntries] Creating entries from ids [1]: "9710". biodb.DEBUG[2024-07-06 16:02:43.580][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:43.583][cch$loadFileContent] Trying to load 1 files from cache: [1]: "9710". biodb.TRACE[2024-07-06 16:02:43.585][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:43.586][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:43.588][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:43.590][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:43.592][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:43.593][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:43.597][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:43.598][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:43.599][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:43.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:43.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:43.607][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:43.608][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:43.610][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=9710". biodb.DEBUG[2024-07-06 16:02:43.613][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:43.614][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:43.615][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=9710". biodb.TRACE[2024-07-06 16:02:44.020][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=9710). biodb.DEBUG[2024-07-06 16:02:44.451][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:44.455][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b7c920ea46a15bb7175f778579142c91.content" biodb.TRACE[2024-07-06 16:02:44.462][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b7c920ea46a15bb7175f778579142c91.request" biodb.TRACE[2024-07-06 16:02:44.467][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9710.xml" biodb.DEBUG[2024-07-06 16:02:44.470][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:44.473][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:44.475][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:44.478][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:44.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:44.482][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:44.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:44.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:44.495][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:44.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:44.501][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:44.503][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:44.504][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.506][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:44.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:44.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.514][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:44.515][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:44.517][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.518][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.519][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:44.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:44.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.524][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:44.526][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:44.532][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.539][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.541][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:44.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:44.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.545][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:44.545][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:44.546][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.547][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.548][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:44.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:44.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.552][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:44.553][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:44.554][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.555][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.556][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:44.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:44.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.559][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:44.560][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:44.561][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.562][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.563][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:44.564][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:44.565][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.566][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.567][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:44.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:44.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.570][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:44.571][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:44.572][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.573][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:44.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:44.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.578][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:44.579][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:44.580][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.580][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:44.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:44.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.585][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:44.586][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:44.587][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.588][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.589][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:44.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:44.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.592][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:44.593][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:44.594][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.595][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.596][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:44.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:44.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.600][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:44.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:44.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:44.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:44.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:44.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:44.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:44.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:44.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.614][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:44.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:44.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:44.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:44.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:44.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:44.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.625][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:44.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:44.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.628][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:44.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:44.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.632][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:44.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:44.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:44.635][self$createEntryFromContent] Accession numbers: 9710. biodb.TRACE[2024-07-06 16:02:44.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:44.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:44.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.639][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:44.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:44.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.642][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:44.643][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:44.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:44.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:44.646][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:44.647][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:44.647][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:44.648][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:44.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:44.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:44.654][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:44.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:44.656][private$loadEntries] Creating entries from ids [1]: "65530". biodb.DEBUG[2024-07-06 16:02:44.657][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:44.658][cch$loadFileContent] Trying to load 1 files from cache: [1]: "65530". biodb.TRACE[2024-07-06 16:02:44.659][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:44.660][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:44.661][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:44.662][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:44.663][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:44.664][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:44.666][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:44.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:44.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:44.672][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:44.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:44.674][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:44.674][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:44.675][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65530". biodb.DEBUG[2024-07-06 16:02:44.678][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:44.679][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:44.680][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65530". biodb.TRACE[2024-07-06 16:02:45.095][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65530). biodb.DEBUG[2024-07-06 16:02:45.563][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:45.580][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/bb7ff6c0bdfa280406af23f96ee06f80.content" biodb.TRACE[2024-07-06 16:02:45.587][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/bb7ff6c0bdfa280406af23f96ee06f80.request" biodb.TRACE[2024-07-06 16:02:45.593][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65530.xml" biodb.DEBUG[2024-07-06 16:02:45.595][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:45.598][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:45.601][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:45.604][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:45.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:45.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:45.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:45.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:45.618][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:45.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:45.623][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:45.625][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:45.626][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.627][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:45.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:45.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.634][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:45.635][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:45.636][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.637][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.639][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:45.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:45.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.642][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.643][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:45.645][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:45.646][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.646][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.648][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:45.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:45.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.652][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:45.653][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:45.654][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.655][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.656][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:45.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:45.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.659][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:45.660][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:45.661][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.662][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:45.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:45.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.667][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:45.667][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:45.668][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.669][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.670][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:45.671][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:45.672][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.673][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.674][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:45.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:45.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.677][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:45.678][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:45.679][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.680][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:45.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:45.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.685][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:45.686][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:45.686][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.687][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:45.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:45.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.692][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:45.693][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:45.694][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.695][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.696][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:45.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:45.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.699][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:45.700][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:45.701][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.702][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.703][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:45.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:45.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:45.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:45.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.709][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:45.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:45.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.713][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:45.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:45.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.716][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.717][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:45.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:45.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:45.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:45.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:45.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:45.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:45.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:45.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.730][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:45.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:45.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:45.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:45.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:45.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:45.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:45.742][self$createEntryFromContent] Accession numbers: 65530. biodb.TRACE[2024-07-06 16:02:45.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:45.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:45.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:45.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:45.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:45.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:45.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:45.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:45.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:45.754][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:45.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:45.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:45.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:45.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:45.769][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:45.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:45.770][private$loadEntries] Creating entries from ids [1]: "72338". biodb.DEBUG[2024-07-06 16:02:45.771][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:45.773][cch$loadFileContent] Trying to load 1 files from cache: [1]: "72338". biodb.TRACE[2024-07-06 16:02:45.774][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:45.775][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:45.776][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:45.777][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:45.778][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:45.778][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:45.781][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:45.781][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:45.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:45.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:45.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:45.788][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:45.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:45.790][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=72338". biodb.DEBUG[2024-07-06 16:02:45.792][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:45.793][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:45.794][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=72338". biodb.TRACE[2024-07-06 16:02:46.192][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=72338). biodb.DEBUG[2024-07-06 16:02:46.627][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:46.631][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e64dda61e0a44a21c5b0eb3609a4a7b.content" biodb.TRACE[2024-07-06 16:02:46.638][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e64dda61e0a44a21c5b0eb3609a4a7b.request" biodb.TRACE[2024-07-06 16:02:46.644][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/72338.xml" biodb.DEBUG[2024-07-06 16:02:46.647][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:46.649][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:46.652][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:46.655][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:46.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:46.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:46.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:46.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:46.672][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:46.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:46.678][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:46.679][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:46.681][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.682][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.684][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:46.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:46.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.690][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:46.692][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:46.693][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.694][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.696][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:46.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:46.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.701][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:46.702][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:46.703][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.704][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.705][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:46.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:46.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.710][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:46.711][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:46.712][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.713][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.714][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:46.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:46.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.718][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:46.719][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:46.720][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.720][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.721][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:46.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:46.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.725][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:46.726][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:46.727][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.728][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.729][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:46.730][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:46.731][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.731][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.732][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:46.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:46.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.736][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:46.737][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:46.738][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.739][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.740][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:46.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:46.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.743][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:46.744][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:46.745][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.746][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.747][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:46.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:46.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.751][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:46.752][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:46.753][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.754][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.755][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:46.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:46.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.759][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:46.759][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:46.760][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.761][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.762][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:46.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:46.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:46.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:46.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.770][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:46.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:46.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:46.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:46.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.777][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:46.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:46.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:46.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:46.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:46.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:46.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:46.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:46.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.800][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:46.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:46.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:46.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:46.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:46.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:46.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:46.811][self$createEntryFromContent] Accession numbers: 72338. biodb.TRACE[2024-07-06 16:02:46.812][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:46.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:46.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.816][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:46.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:46.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:46.819][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:46.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:46.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:46.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:46.823][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:46.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:46.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:46.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:46.829][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:46.830][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:46.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:46.831][private$loadEntries] Creating entries from ids [1]: "77926". biodb.DEBUG[2024-07-06 16:02:46.832][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:46.834][cch$loadFileContent] Trying to load 1 files from cache: [1]: "77926". biodb.TRACE[2024-07-06 16:02:46.835][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:46.836][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:46.837][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:46.838][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:46.839][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:46.839][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:46.842][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:46.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:46.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:46.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:46.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:46.849][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:46.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:46.851][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77926". biodb.DEBUG[2024-07-06 16:02:46.853][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:46.854][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:46.855][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77926". biodb.TRACE[2024-07-06 16:02:47.258][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77926). biodb.DEBUG[2024-07-06 16:02:47.691][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:47.695][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9ad4fcb4fcba98dcbec5ee6292352f7b.content" biodb.TRACE[2024-07-06 16:02:47.702][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9ad4fcb4fcba98dcbec5ee6292352f7b.request" biodb.TRACE[2024-07-06 16:02:47.707][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/77926.xml" biodb.DEBUG[2024-07-06 16:02:47.710][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:47.713][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:47.715][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:47.718][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:47.720][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:47.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:47.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:47.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:47.735][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:47.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:47.740][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:47.742][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:47.744][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.745][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.747][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:47.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:47.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.753][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:47.755][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:47.756][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.757][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.759][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:47.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:47.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.764][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:47.765][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:47.766][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.767][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.769][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:47.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:47.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.773][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:47.774][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:47.775][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.776][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:47.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:47.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.781][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:47.782][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:47.783][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.784][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.785][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:47.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:47.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.789][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:47.790][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:47.791][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.792][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.793][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:47.794][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:47.795][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.795][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.797][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:47.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:47.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.800][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:47.801][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:47.802][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.803][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:47.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:47.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.807][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:47.808][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:47.809][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.818][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:47.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:47.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.823][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:47.824][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:47.825][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.826][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.827][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:47.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:47.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.831][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:47.832][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:47.832][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.833][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.834][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:47.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:47.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:47.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:47.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.841][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:47.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:47.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:47.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:47.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:47.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:47.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.852][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:47.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:47.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:47.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:47.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:47.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:47.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:47.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:47.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.866][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:47.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:47.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:47.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:47.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:47.873][self$createEntryFromContent] Accession numbers: 77926. biodb.TRACE[2024-07-06 16:02:47.874][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:47.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:47.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.877][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:47.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:47.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:47.881][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:47.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:47.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:47.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:47.884][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:47.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:47.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:47.890][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:47.891][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:47.891][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:47.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:47.893][private$loadEntries] Creating entries from ids [1]: "82369". biodb.DEBUG[2024-07-06 16:02:47.894][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:47.896][cch$loadFileContent] Trying to load 1 files from cache: [1]: "82369". biodb.TRACE[2024-07-06 16:02:47.897][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:47.898][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:47.899][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:47.899][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:47.900][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:47.901][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:47.904][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:47.904][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:47.905][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:47.909][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:47.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:47.911][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:47.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:47.912][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=82369". biodb.DEBUG[2024-07-06 16:02:47.915][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:47.916][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:47.917][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=82369". biodb.TRACE[2024-07-06 16:02:48.310][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=82369). biodb.DEBUG[2024-07-06 16:02:48.778][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:48.782][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/141011223a89b45316c20d1fd91b47fd.content" biodb.TRACE[2024-07-06 16:02:48.789][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/141011223a89b45316c20d1fd91b47fd.request" biodb.TRACE[2024-07-06 16:02:48.794][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/82369.xml" biodb.DEBUG[2024-07-06 16:02:48.797][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:48.800][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:48.802][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:48.805][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:48.807][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:48.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:48.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:48.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:48.822][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:48.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:48.827][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:48.829][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:48.830][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.832][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:48.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:48.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.840][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:48.841][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:48.842][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.843][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.845][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:48.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:48.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.850][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:48.851][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:48.853][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.854][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.855][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:48.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:48.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.859][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:48.860][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:48.869][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.870][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.871][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:48.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:48.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.875][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:48.876][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:48.877][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.878][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.879][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:48.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:48.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.883][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:48.884][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:48.885][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.885][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.887][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:48.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:48.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.890][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:48.891][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:48.892][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.893][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.894][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:48.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:48.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.896][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.897][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:48.898][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:48.899][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.900][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:48.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:48.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.905][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:48.906][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:48.906][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.907][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.909][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:48.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:48.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.912][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:48.913][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:48.914][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.915][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.916][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:48.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:48.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.919][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:48.920][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:48.921][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.922][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.923][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:48.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:48.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.927][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:48.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:48.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:48.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:48.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:48.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:48.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:48.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:48.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:48.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:48.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:48.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:48.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:48.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:48.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:48.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:48.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:48.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:48.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:48.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:48.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:48.962][self$createEntryFromContent] Accession numbers: 82369. biodb.TRACE[2024-07-06 16:02:48.963][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:48.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:48.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.966][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:48.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:48.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:48.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:48.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:48.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:48.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:48.973][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:48.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:48.975][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:48.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:48.980][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:48.981][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:48.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:48.982][private$loadEntries] Creating entries from ids [1]: "90204". biodb.DEBUG[2024-07-06 16:02:48.983][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:48.985][cch$loadFileContent] Trying to load 1 files from cache: [1]: "90204". biodb.TRACE[2024-07-06 16:02:48.986][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:48.987][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:48.988][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:48.989][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:48.990][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:48.991][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:48.993][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:48.994][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:48.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:48.999][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:49.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:49.001][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:49.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:49.003][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=90204". biodb.DEBUG[2024-07-06 16:02:49.005][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:49.006][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:49.007][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=90204". biodb.TRACE[2024-07-06 16:02:49.399][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=90204). biodb.DEBUG[2024-07-06 16:02:49.868][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:49.871][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/bd50d349ae7e6e2bbccffc7e4e5f18de.content" biodb.TRACE[2024-07-06 16:02:49.877][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/bd50d349ae7e6e2bbccffc7e4e5f18de.request" biodb.TRACE[2024-07-06 16:02:49.892][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/90204.xml" biodb.DEBUG[2024-07-06 16:02:49.894][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:49.896][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:49.899][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:49.901][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:49.903][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:49.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:49.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:49.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:49.914][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:49.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:49.919][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:49.920][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:49.921][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.923][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:49.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:49.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.929][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:49.931][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:49.932][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.933][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.934][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:49.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:49.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.939][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:49.940][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:49.941][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.942][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.943][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:49.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:49.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.947][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:49.948][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:49.949][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.950][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.951][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:49.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:49.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.955][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:49.955][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:49.956][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.957][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.958][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:49.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:49.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.962][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:49.963][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:49.964][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.964][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.965][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:49.966][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:49.967][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.968][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.969][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:49.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:49.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.973][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:49.974][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:49.974][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.975][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.976][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:49.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:49.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.980][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:49.981][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:49.982][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.982][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.984][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:49.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:49.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.987][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:49.988][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:49.989][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.990][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.991][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:49.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:49.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.994][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:49.995][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:49.996][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:49.997][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:49.998][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:49.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:50.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:50.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:50.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:50.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:50.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:50.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:50.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:50.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:50.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:50.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:50.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:50.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:50.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:50.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:50.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:50.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:50.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:50.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:50.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:50.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:50.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.036][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:50.037][self$createEntryFromContent] Accession numbers: 90204. biodb.TRACE[2024-07-06 16:02:50.038][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:50.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:50.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:50.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:50.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:50.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:50.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:50.049][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:50.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:50.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:50.054][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:50.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:50.060][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:50.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:50.063][private$loadEntries] Creating entries from ids [1]: "132793". biodb.DEBUG[2024-07-06 16:02:50.064][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:50.065][cch$loadFileContent] Trying to load 1 files from cache: [1]: "132793". biodb.TRACE[2024-07-06 16:02:50.066][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:50.067][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:50.068][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:50.069][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:50.070][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:50.071][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:50.073][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:50.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:50.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:50.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:50.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:50.081][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:50.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:50.082][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132793". biodb.DEBUG[2024-07-06 16:02:50.085][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:50.086][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:50.087][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132793". biodb.TRACE[2024-07-06 16:02:50.486][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132793). biodb.DEBUG[2024-07-06 16:02:50.910][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:50.914][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a797bec3bbec3ca7a5b4b96140b735a3.content" biodb.TRACE[2024-07-06 16:02:50.921][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a797bec3bbec3ca7a5b4b96140b735a3.request" biodb.TRACE[2024-07-06 16:02:50.926][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/132793.xml" biodb.DEBUG[2024-07-06 16:02:50.929][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:50.932][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:50.934][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:50.937][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:50.939][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:50.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:50.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:50.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:50.954][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:50.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:50.959][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:50.961][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:50.962][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.964][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:50.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:50.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.971][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:50.973][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:50.974][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.975][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.977][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:50.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:50.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.982][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:50.983][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:50.984][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.985][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.987][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:50.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:50.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.991][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:50.992][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:50.993][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.994][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.995][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:50.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:50.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:50.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:50.999][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:51.000][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:51.001][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.002][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.003][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:51.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:51.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.007][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:51.008][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:51.008][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.009][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.010][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:51.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:51.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.013][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.014][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:51.015][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:51.016][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.017][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.018][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:51.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:51.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.021][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:51.022][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:51.023][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.024][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:51.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:51.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.028][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:51.029][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:51.030][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.031][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.032][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:51.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:51.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.036][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:51.037][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:51.038][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.039][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.040][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:51.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:51.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.043][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:51.044][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:51.045][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.046][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.047][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:51.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:51.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.051][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:51.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:51.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.062][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:51.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:51.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:51.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:51.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:51.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:51.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:51.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:51.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:51.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:51.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:51.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:51.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:51.096][self$createEntryFromContent] Accession numbers: 132793. biodb.TRACE[2024-07-06 16:02:51.097][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:51.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:51.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.100][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:51.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:51.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:51.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:51.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:51.107][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:51.109][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:51.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:51.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:51.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:51.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:51.116][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:51.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:51.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.125][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:51.126][private$selectFields] biodb.TRACE[2024-07-06 16:02:51.126][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:51.127][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:51.128][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:51.129][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.130][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.131][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.132][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.132][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.133][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.134][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.135][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.136][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:51.137][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:51.138][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.139][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.139][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.140][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.141][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:51.142][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.146][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.152][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.153][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [65530]. biodb.DEBUG[2024-07-06 16:02:51.154][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:51.155][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:51.156][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:51.160][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:51.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:51.161][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:51.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:51.163][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.167][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.170][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:51.171][private$selectFields] biodb.TRACE[2024-07-06 16:02:51.172][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:51.172][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:51.173][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:51.174][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.175][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.176][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.177][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.178][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.179][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.179][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.180][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.181][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:51.182][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:51.183][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.184][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.185][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.185][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.186][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:51.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.198][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [90204]. biodb.DEBUG[2024-07-06 16:02:51.199][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:51.200][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:51.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:51.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:51.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:51.207][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:51.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:51.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.216][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:51.217][private$selectFields] biodb.TRACE[2024-07-06 16:02:51.217][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:51.218][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:51.219][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:51.220][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.225][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.226][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.227][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.228][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.230][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.230][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.231][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.232][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:51.233][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:51.234][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.235][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.236][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.237][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.237][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:51.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.242][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:51.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:51.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:51.249][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [132793]. biodb.DEBUG[2024-07-06 16:02:51.250][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:51.251][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:02:51.252][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:51.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:51.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:51.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:51.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:51.259][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:51.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:51.263][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:51.266][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:51.266][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:51.268][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:02:51.662][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:02:52.083][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:52.087][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9686ce9c957a368dd8f5b4cc9c5b15b3.content" biodb.TRACE[2024-07-06 16:02:52.095][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9686ce9c957a368dd8f5b4cc9c5b15b3.request" biodb.DEBUG[2024-07-06 16:02:52.100][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:52.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:52.104][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:52.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:52.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:52.117][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:52.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:52.122][private$loadEntries] Creating entries from ids [1]: "131378". biodb.DEBUG[2024-07-06 16:02:52.124][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:52.127][cch$loadFileContent] Trying to load 1 files from cache: [1]: "131378". biodb.TRACE[2024-07-06 16:02:52.129][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:52.131][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:52.133][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:52.134][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:52.136][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:52.137][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:52.141][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:52.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:52.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:52.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:52.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:52.152][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:52.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:52.154][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=131378". biodb.DEBUG[2024-07-06 16:02:52.158][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:52.159][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:52.160][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=131378". biodb.TRACE[2024-07-06 16:02:52.564][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=131378). biodb.DEBUG[2024-07-06 16:02:52.998][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:53.002][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5b759b1dd2dc96585e60782e41aa0772.content" biodb.TRACE[2024-07-06 16:02:53.009][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5b759b1dd2dc96585e60782e41aa0772.request" biodb.TRACE[2024-07-06 16:02:53.014][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/131378.xml" biodb.DEBUG[2024-07-06 16:02:53.017][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:53.020][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:53.022][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:53.026][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:53.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:53.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:53.038][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:53.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:53.042][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:53.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:53.048][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:53.049][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:53.051][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.053][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:53.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:53.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.061][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:53.062][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:53.063][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.065][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.066][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:53.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:53.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.071][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:53.073][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:53.074][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.075][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.076][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:53.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:53.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.081][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:53.082][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:53.083][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.084][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.085][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:53.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:53.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.089][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:53.090][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:53.091][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.092][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:53.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:53.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.097][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:53.108][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:53.109][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.110][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.112][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:53.113][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:53.114][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.115][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.116][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:53.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:53.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.119][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:53.120][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:53.121][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.122][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:53.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:53.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.127][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:53.128][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:53.128][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.129][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.131][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:53.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:53.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.134][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:53.135][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:53.136][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.137][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.138][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:53.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:53.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.142][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:53.142][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:53.143][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.144][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.145][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:53.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:53.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.149][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:53.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:53.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.152][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:53.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:53.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:53.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:53.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:53.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:53.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:53.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:53.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:53.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:53.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.170][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:53.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:53.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:53.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:53.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:53.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:53.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.181][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:53.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:53.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:53.184][self$createEntryFromContent] Accession numbers: 131378. biodb.TRACE[2024-07-06 16:02:53.185][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:53.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:53.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:53.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:53.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:53.192][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:53.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:53.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:53.195][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:53.196][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:53.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:53.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:53.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:53.202][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:53.203][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:53.204][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:53.205][private$loadEntries] Creating entries from ids [1]: "214202". biodb.DEBUG[2024-07-06 16:02:53.206][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:53.207][cch$loadFileContent] Trying to load 1 files from cache: [1]: "214202". biodb.TRACE[2024-07-06 16:02:53.208][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:53.209][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:53.210][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:53.211][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:53.212][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:53.213][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:53.215][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:53.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:53.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:53.221][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:53.222][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:53.222][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:53.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:53.224][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=214202". biodb.DEBUG[2024-07-06 16:02:53.227][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:53.228][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:53.229][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=214202". biodb.TRACE[2024-07-06 16:02:53.626][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=214202). biodb.DEBUG[2024-07-06 16:02:54.069][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:54.074][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf9a3fb7c59af59e06fd510ceb170574.content" biodb.TRACE[2024-07-06 16:02:54.080][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf9a3fb7c59af59e06fd510ceb170574.request" biodb.TRACE[2024-07-06 16:02:54.086][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/214202.xml" biodb.DEBUG[2024-07-06 16:02:54.089][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:54.091][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:54.094][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:54.097][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:54.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:54.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:54.110][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:54.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:54.113][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:54.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:54.119][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:54.121][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:54.133][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.134][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:54.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:54.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.141][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:54.143][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:54.144][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.145][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.146][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:54.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:54.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.151][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:54.152][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:54.153][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.154][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.155][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:54.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:54.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.159][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:54.160][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:54.161][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.162][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.163][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:54.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:54.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.167][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:54.168][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:54.168][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.169][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.170][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:54.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:54.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.174][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:54.175][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:54.176][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.177][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.178][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:54.179][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:54.179][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.180][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.181][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:54.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:54.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.185][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:54.186][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:54.187][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.188][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.189][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:54.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:54.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.192][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:54.193][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:54.194][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.195][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.196][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:54.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:54.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.200][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:54.201][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:54.201][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.202][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.203][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:54.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:54.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.206][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.207][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:54.208][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:54.209][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.210][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.211][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:54.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:54.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.213][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:54.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:54.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:54.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:54.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:54.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:54.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.224][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.225][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:54.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:54.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.228][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:54.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:54.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:54.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:54.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:54.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:54.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.239][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:54.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:54.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:54.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:54.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:54.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:54.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:54.250][self$createEntryFromContent] Accession numbers: 214202. biodb.TRACE[2024-07-06 16:02:54.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:54.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:54.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:54.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:54.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:54.258][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:54.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:54.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:54.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:54.262][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.2*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:54.265][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:54.266][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:54.267][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.2%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:02:54.666][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.2%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:02:55.098][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:55.103][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5d833e77a1be58060d0c3916a1e1b293.content" biodb.TRACE[2024-07-06 16:02:55.111][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5d833e77a1be58060d0c3916a1e1b293.request" biodb.DEBUG[2024-07-06 16:02:55.116][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:55.118][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:55.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:55.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:55.144][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:55.146][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:55.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:55.150][private$loadEntries] Creating entries from ids [1]: "51836". biodb.DEBUG[2024-07-06 16:02:55.152][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:55.155][cch$loadFileContent] Trying to load 1 files from cache: [1]: "51836". biodb.TRACE[2024-07-06 16:02:55.157][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:55.158][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:55.160][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:55.161][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:55.163][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:55.164][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:55.167][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:55.168][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:55.170][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:55.175][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:55.176][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:55.177][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:55.178][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:55.179][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51836". biodb.DEBUG[2024-07-06 16:02:55.182][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:55.183][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:55.185][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51836". biodb.TRACE[2024-07-06 16:02:55.588][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51836). biodb.DEBUG[2024-07-06 16:02:55.994][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:55.996][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1fe2079ad59bca4bc82b2cd14ed8e8a1.content" biodb.TRACE[2024-07-06 16:02:55.999][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1fe2079ad59bca4bc82b2cd14ed8e8a1.request" biodb.TRACE[2024-07-06 16:02:56.001][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/51836.xml" biodb.DEBUG[2024-07-06 16:02:56.003][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:56.004][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:56.005][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:56.006][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:56.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:56.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:56.012][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:56.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:56.014][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:56.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:56.017][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:56.018][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:56.019][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.020][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:56.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:56.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.025][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:56.026][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:56.026][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.027][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.029][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:56.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:56.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.032][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:56.033][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:56.034][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.035][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.036][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:56.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:56.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.040][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:56.041][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:56.042][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.043][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.044][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:56.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:56.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.048][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:56.049][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:56.049][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.050][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.051][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:56.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:56.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.055][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:56.056][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:56.057][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.057][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.058][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:56.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:56.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.062][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:56.063][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:56.064][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.065][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.066][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:56.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:56.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.069][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:56.070][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:56.071][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.072][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:56.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:56.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.077][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:56.078][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:56.079][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.080][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.081][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:56.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:56.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.084][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:56.085][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:56.086][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.087][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.088][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:56.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:56.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.092][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:56.093][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:56.094][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.095][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.096][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:56.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:56.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:56.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:56.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:56.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:56.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:56.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:56.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:56.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:56.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.121][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:56.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:56.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:56.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:56.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:56.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:56.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:56.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:56.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:56.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:56.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.140][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:56.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:56.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:56.143][self$createEntryFromContent] Accession numbers: 51836. biodb.TRACE[2024-07-06 16:02:56.144][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:56.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:56.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.147][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.148][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:56.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:56.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:56.151][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:56.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:56.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:56.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:56.155][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:56.156][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:56.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:56.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:56.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:56.162][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:56.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:56.164][private$loadEntries] Creating entries from ids [1]: "51837". biodb.DEBUG[2024-07-06 16:02:56.165][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:56.166][cch$loadFileContent] Trying to load 1 files from cache: [1]: "51837". biodb.TRACE[2024-07-06 16:02:56.167][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:56.168][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:56.169][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:56.170][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:56.171][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:56.172][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:56.174][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:56.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:56.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:56.180][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:56.181][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:56.182][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:56.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:56.183][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51837". biodb.DEBUG[2024-07-06 16:02:56.186][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:56.187][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:56.188][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51837". biodb.TRACE[2024-07-06 16:02:56.606][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51837). biodb.DEBUG[2024-07-06 16:02:56.994][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:56.996][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1588f004fb5de8667ae1af7433b2932e.content" biodb.TRACE[2024-07-06 16:02:56.999][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1588f004fb5de8667ae1af7433b2932e.request" biodb.TRACE[2024-07-06 16:02:57.001][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/51837.xml" biodb.DEBUG[2024-07-06 16:02:57.002][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:57.003][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:57.004][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:57.006][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:57.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:57.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:57.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:57.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:57.013][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:57.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:57.016][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:57.017][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:57.018][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.019][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:57.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:57.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.023][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:57.024][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:57.025][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.026][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.027][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:57.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:57.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.031][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:57.032][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:57.032][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.033][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.034][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:57.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:57.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.038][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:57.039][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:57.040][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.041][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.042][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:57.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:57.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.045][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:57.046][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:57.047][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.048][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.049][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:57.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:57.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.053][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:57.054][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:57.055][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.055][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.057][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:57.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:57.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.060][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:57.061][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:57.062][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.063][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.064][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:57.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:57.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.068][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:57.069][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:57.069][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.070][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:57.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:57.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.084][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:57.085][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:57.085][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.086][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:57.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:57.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.091][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:57.092][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:57.093][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.094][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.095][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:57.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:57.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.098][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:57.099][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:57.100][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.101][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.102][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:57.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:57.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:57.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:57.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:57.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:57.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:57.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:57.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:57.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:57.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:57.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:57.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:57.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:57.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:57.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:57.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.130][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:57.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:57.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.133][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:57.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:57.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.137][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:57.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:57.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:57.141][self$createEntryFromContent] Accession numbers: 51837. biodb.TRACE[2024-07-06 16:02:57.142][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:57.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:57.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.145][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:57.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:57.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:57.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:57.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:57.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:57.152][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:57.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:57.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:57.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:57.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:57.159][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:57.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:57.161][private$loadEntries] Creating entries from ids [1]: "132205". biodb.DEBUG[2024-07-06 16:02:57.162][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:02:57.164][cch$loadFileContent] Trying to load 1 files from cache: [1]: "132205". biodb.TRACE[2024-07-06 16:02:57.165][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:02:57.166][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:02:57.167][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:02:57.168][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:02:57.168][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:02:57.169][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:02:57.172][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:57.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:57.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:57.177][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:57.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:57.179][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:57.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:57.181][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132205". biodb.DEBUG[2024-07-06 16:02:57.183][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:57.184][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:57.185][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132205". biodb.TRACE[2024-07-06 16:02:57.579][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132205). biodb.DEBUG[2024-07-06 16:02:57.975][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:02:57.977][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0bfa2ac1d845d7db5b781e9a39528bb3.content" biodb.TRACE[2024-07-06 16:02:57.980][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0bfa2ac1d845d7db5b781e9a39528bb3.request" biodb.TRACE[2024-07-06 16:02:57.982][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/132205.xml" biodb.DEBUG[2024-07-06 16:02:57.983][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:02:57.984][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:02:57.985][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:02:57.987][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:57.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:57.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:57.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:57.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:57.994][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:57.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:57.997][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:57.998][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:57.998][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:57.999][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:58.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:58.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.004][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:58.005][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:58.006][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.007][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.008][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:02:58.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:02:58.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.011][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:58.020][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:58.021][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.022][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.023][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:02:58.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:02:58.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.027][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:58.028][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:58.029][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.030][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.031][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:02:58.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:02:58.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.035][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:58.035][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:58.036][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.037][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.038][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:02:58.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:02:58.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.042][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:58.043][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:02:58.044][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.044][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.045][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:58.046][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.047][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.048][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.049][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:02:58.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.053][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:58.054][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:58.055][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.055][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:58.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:02:58.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.060][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:58.061][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:58.062][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.063][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.064][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:02:58.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:02:58.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.067][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:58.068][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:58.069][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.070][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.071][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:02:58.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:02:58.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.075][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:58.076][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:58.076][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.077][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.078][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:02:58.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:02:58.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.082][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.089][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:58.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:58.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:58.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:58.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:58.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:58.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.103][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:58.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:58.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:58.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:58.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:58.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:58.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:02:58.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:02:58.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.117][self$createEntryFromContent] Accession numbers: 132205. biodb.TRACE[2024-07-06 16:02:58.118][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.121][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.125][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.129][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:58.130][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.137][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.142][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.143][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.146][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.147][private$selectFields] biodb.TRACE[2024-07-06 16:02:58.148][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:58.149][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:58.150][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.151][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.152][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.152][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.153][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.154][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.155][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.156][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.157][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.158][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.159][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.159][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.160][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.161][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.162][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.163][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:58.168][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.176][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.180][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [51836]. biodb.DEBUG[2024-07-06 16:02:58.181][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.182][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.183][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.188][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.197][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.198][private$selectFields] biodb.TRACE[2024-07-06 16:02:58.199][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:58.200][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:58.200][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.201][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.202][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.203][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.204][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.205][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.206][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.206][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.207][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.208][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.209][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.210][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.211][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.212][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.212][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.213][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:58.214][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.218][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.221][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.224][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.225][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [51837]. biodb.DEBUG[2024-07-06 16:02:58.226][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.233][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.238][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.242][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.243][private$selectFields] biodb.TRACE[2024-07-06 16:02:58.244][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:58.244][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:58.245][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.246][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.247][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.248][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.249][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.250][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.251][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.251][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.252][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.253][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.254][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.255][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.256][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.257][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.257][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.258][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:58.259][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.266][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.270][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [132205]. biodb.DEBUG[2024-07-06 16:02:58.271][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:58.272][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:02:58.288][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.293][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.295][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:58.298][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:58.301][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:58.302][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-07-06 16:02:58.303][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:58.304][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-07-06 16:02:58.306][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.316][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.318][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.323][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.324][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.327][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.327][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.332][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:58.334][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:58.336][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-07-06 16:02:58.337][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:58.338][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-07-06 16:02:58.340][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.347][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.359][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.360][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.366][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.371][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.375][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.378][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:58.380][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.381][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.386][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.386][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.387][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.396][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.397][private$selectFields] biodb.TRACE[2024-07-06 16:02:58.398][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:58.399][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:58.399][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.400][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.401][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.402][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.403][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.404][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.405][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.405][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.406][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.407][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.408][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.409][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.410][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.411][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.411][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.412][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:58.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.416][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.417][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.424][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288]. biodb.DEBUG[2024-07-06 16:02:58.425][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.426][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.430][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.432][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.434][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.437][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.438][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.441][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.442][private$selectFields] biodb.TRACE[2024-07-06 16:02:58.443][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:58.444][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:58.445][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.445][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.446][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.447][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.448][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.449][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.450][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.451][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.452][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.453][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.453][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.454][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.455][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.456][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.457][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.458][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:58.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.466][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.471][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.475][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-07-06 16:02:58.476][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.477][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.478][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.483][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.484][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.491][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.492][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.493][private$selectFields] biodb.TRACE[2024-07-06 16:02:58.493][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:58.494][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:58.495][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.496][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.497][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.498][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.499][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.499][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.500][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.501][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.502][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.503][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.504][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.505][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.506][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.506][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.507][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.508][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:58.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.520][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892]. biodb.DEBUG[2024-07-06 16:02:58.521][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:58.521][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:02:58.523][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.524][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.529][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.530][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:58.533][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:58.536][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:58.537][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b3cd8ddf08f509014f10dc9bf7c1649d". biodb.TRACE[2024-07-06 16:02:58.538][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:58.539][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b3cd8ddf08f509014f10dc9bf7c1649d.content". biodb.DEBUG[2024-07-06 16:02:58.541][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.547][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.548][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.554][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.561][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.567][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.569][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.573][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.576][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.581][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:58.583][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:58.585][cch$loadFileContent] Trying to load 1 files from cache: [1]: "831507e33c6cf42061851262412f5feb". biodb.TRACE[2024-07-06 16:02:58.586][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:58.587][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/831507e33c6cf42061851262412f5feb.content". biodb.DEBUG[2024-07-06 16:02:58.589][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.596][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.614][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.615][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.620][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.621][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.623][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.626][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.627][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.634][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.635][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.635][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.639][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.640][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.641][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.641][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.645][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.653][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:58.654][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.656][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.660][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.661][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.670][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.671][private$selectFields] biodb.TRACE[2024-07-06 16:02:58.672][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:58.672][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:58.673][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.674][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.675][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.676][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.677][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.678][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.678][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.679][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.680][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.681][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.682][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.683][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.684][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.684][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.685][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.686][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:58.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.693][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.697][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.698][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-07-06 16:02:58.699][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.706][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.714][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.715][private$selectFields] biodb.TRACE[2024-07-06 16:02:58.716][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:58.717][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:58.718][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.719][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.720][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.720][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.721][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.722][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.723][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.724][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.725][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.726][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.727][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.727][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.728][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.729][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.730][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.731][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:58.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.743][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-07-06 16:02:58.744][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.751][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.765][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.766][private$selectFields] biodb.TRACE[2024-07-06 16:02:58.767][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:58.768][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:58.769][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.770][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.771][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.771][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.772][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.773][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.774][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.775][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.776][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.777][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.777][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:58.778][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.779][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.780][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.781][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.782][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:58.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:58.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.793][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [19804]. biodb.DEBUG[2024-07-06 16:02:58.794][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:58.795][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:02:58.797][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.804][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:58.807][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:58.810][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:58.811][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26d0872875c47c33e8205aa7124e0486". biodb.TRACE[2024-07-06 16:02:58.812][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:58.813][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26d0872875c47c33e8205aa7124e0486.content". biodb.DEBUG[2024-07-06 16:02:58.815][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.822][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.834][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.840][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.841][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.843][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.846][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.854][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.860][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.869][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.873][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.873][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.878][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.880][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.884][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.892][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.899][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.909][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.914][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.918][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.923][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.925][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.926][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.933][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.937][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.938][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.944][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.945][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.946][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.953][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.956][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.957][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.963][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.964][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.972][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:58.976][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:58.979][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:02:58.980][cch$loadFileContent] Trying to load 1 files from cache: [1]: "357534c211a0779cb44e196fcebae6c0". biodb.TRACE[2024-07-06 16:02:58.981][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:02:58.982][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/357534c211a0779cb44e196fcebae6c0.content". biodb.DEBUG[2024-07-06 16:02:58.984][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:58.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:58.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:58.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:58.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:58.991][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:58.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:58.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:58.997][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:58.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:58.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.000][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:59.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:59.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:59.004][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:59.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:59.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:59.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:59.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:59.011][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:59.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:59.012][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:59.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:59.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:59.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:59.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.020][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:59.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:59.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:59.023][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:59.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:59.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:59.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:59.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:59.030][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:59.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:59.032][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:59.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:59.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.036][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:59.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:59.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.038][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:02:59.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:02:59.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:02:59.043][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:02:59.045][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:59.045][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:59.046][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:59.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:59.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:59.057][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:59.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:59.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.063][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.067][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:59.068][private$selectFields] biodb.TRACE[2024-07-06 16:02:59.068][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:59.069][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:59.070][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:59.071][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.072][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.073][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.074][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.075][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.075][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.076][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.077][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.078][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:59.079][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:59.080][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.081][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.082][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.082][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.083][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:59.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.095][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-07-06 16:02:59.096][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:59.097][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:59.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:59.102][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:59.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:59.103][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:59.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:59.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.111][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.112][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:59.113][private$selectFields] biodb.TRACE[2024-07-06 16:02:59.114][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:59.115][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:59.115][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:59.116][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.117][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.118][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.119][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.120][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.121][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.121][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.122][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.123][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:59.124][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:59.125][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.126][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.127][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.128][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.128][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:59.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.140][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [71954]. biodb.DEBUG[2024-07-06 16:02:59.141][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:59.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:59.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:59.147][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:59.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:59.148][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:59.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:02:59.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.157][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:59.158][private$selectFields] biodb.TRACE[2024-07-06 16:02:59.159][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:02:59.159][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:02:59.160][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:59.161][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.162][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.163][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.164][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.165][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.166][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.166][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.167][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.168][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:59.169][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:02:59.170][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.171][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.172][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.172][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.173][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:02:59.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.178][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:02:59.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:02:59.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:02:59.185][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [197612]. biodb.DEBUG[2024-07-06 16:02:59.186][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:02:59.187][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:02:59.214][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:02:59.215][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:02:59.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:02:59.220][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:02:59.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:02:59.221][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:02:59.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:02:59.224][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.7*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:02:59.227][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:02:59.228][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:02:59.230][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.7%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:02:59.619][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.7%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:03:00.030][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:00.034][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2b6f29bb7a7663ff23fb5e7dcae5c27f.content" biodb.TRACE[2024-07-06 16:03:00.042][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2b6f29bb7a7663ff23fb5e7dcae5c27f.request" biodb.DEBUG[2024-07-06 16:03:00.048][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:00.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:00.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:00.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:00.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:00.064][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:00.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:00.069][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:00.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:00.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:00.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:00.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:00.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:00.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:00.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:00.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:00.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:00.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:00.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:00.089][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:00.090][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:00.091][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:00.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:00.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:00.099][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:00.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:00.102][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:00.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:00.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:00.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:00.106][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:00.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:00.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:00.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:00.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:00.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:00.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:00.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:00.115][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:00.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:00.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:00.121][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:00.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:00.122][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:00.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:00.124][private$loadEntries] Creating entries from ids [1]: "28243". biodb.DEBUG[2024-07-06 16:03:00.125][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:00.126][cch$loadFileContent] Trying to load 1 files from cache: [1]: "28243". biodb.TRACE[2024-07-06 16:03:00.127][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:00.128][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:00.129][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:00.130][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:00.131][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:00.132][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:00.134][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:00.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:00.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:00.140][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:00.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:00.142][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:00.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:00.143][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=28243". biodb.DEBUG[2024-07-06 16:03:00.146][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:00.147][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:00.148][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=28243". biodb.TRACE[2024-07-06 16:03:00.540][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=28243). biodb.DEBUG[2024-07-06 16:03:00.977][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:00.981][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/177c3a227615d232b537605885883911.content" biodb.TRACE[2024-07-06 16:03:00.988][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/177c3a227615d232b537605885883911.request" biodb.TRACE[2024-07-06 16:03:00.993][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/28243.xml" biodb.DEBUG[2024-07-06 16:03:00.996][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:00.999][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:01.001][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:01.004][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:01.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:01.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:01.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:01.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:01.021][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:01.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:01.026][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:01.028][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:01.030][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.031][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:01.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:01.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.038][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.039][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:01.041][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:01.042][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.043][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.045][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:01.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:01.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.050][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:01.051][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:01.052][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.054][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.055][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:01.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:01.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.069][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.070][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:01.071][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:01.072][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.073][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.074][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:01.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:01.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.078][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:01.079][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:01.080][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.080][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.082][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:01.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:01.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.085][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:01.086][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:01.087][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.088][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.089][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:01.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:01.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.092][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:01.093][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:01.094][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.095][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.096][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:01.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:01.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.100][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:01.101][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:01.101][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.102][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:01.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:01.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.107][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:01.108][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:01.109][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.109][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.111][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:01.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:01.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.114][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:01.115][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:01.116][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.117][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.118][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:01.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:01.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.121][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:01.122][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:01.123][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.124][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.125][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:01.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:01.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:01.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:01.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:01.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:01.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:01.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:01.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:01.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:01.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.142][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:01.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:01.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:01.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:01.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.149][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:01.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:01.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.152][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.153][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:01.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:01.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:01.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:01.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.160][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:01.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:01.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:01.164][self$createEntryFromContent] Accession numbers: 28243. biodb.TRACE[2024-07-06 16:03:01.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:01.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:01.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:01.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:01.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:01.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:01.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:01.175][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:01.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:01.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:01.181][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:01.182][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:01.182][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:01.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:01.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:01.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:01.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:01.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:01.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:01.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:01.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:01.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:01.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:01.195][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:01.196][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:01.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:01.201][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:01.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:01.202][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:01.203][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:01.204][private$loadEntries] Creating entries from ids [1]: "70786". biodb.DEBUG[2024-07-06 16:03:01.205][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:01.206][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70786". biodb.TRACE[2024-07-06 16:03:01.207][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:01.208][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:01.209][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:01.210][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:01.216][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:01.217][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:01.220][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:01.221][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:01.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:01.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:01.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:01.227][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:01.228][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:01.229][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70786". biodb.DEBUG[2024-07-06 16:03:01.231][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:01.235][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:01.238][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70786". biodb.TRACE[2024-07-06 16:03:01.638][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70786). biodb.DEBUG[2024-07-06 16:03:02.088][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:02.094][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ea24f2a708fc4a90f6eff28b49d993c4.content" biodb.TRACE[2024-07-06 16:03:02.103][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ea24f2a708fc4a90f6eff28b49d993c4.request" biodb.TRACE[2024-07-06 16:03:02.109][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70786.xml" biodb.DEBUG[2024-07-06 16:03:02.112][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:02.116][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:02.119][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:02.123][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:02.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:02.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:02.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:02.141][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:02.142][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:02.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:02.150][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:02.151][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:02.153][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.154][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.156][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:02.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:02.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.161][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:02.163][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:02.164][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.165][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.167][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:02.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:02.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.171][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:02.173][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:02.174][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.175][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.176][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:02.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:02.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.180][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:02.181][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:02.182][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.183][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.184][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:02.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:02.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.188][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:02.189][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:02.190][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.191][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.193][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:02.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:02.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.195][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.196][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:02.197][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:02.198][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.199][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.201][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:02.202][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:02.203][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.204][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.205][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:02.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:02.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.209][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:02.210][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:02.211][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.212][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.213][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:02.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:02.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.217][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:02.218][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:02.219][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.220][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.221][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:02.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:02.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.224][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.225][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:02.226][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:02.227][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.228][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.229][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:02.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:02.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.233][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:02.234][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:02.235][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.236][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.237][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:02.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:02.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.242][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:02.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:02.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:02.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:02.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:02.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:02.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:02.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:02.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:02.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:02.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.262][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:02.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:02.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:02.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:02.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:02.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:02.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:02.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:02.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:02.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:02.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:02.295][self$createEntryFromContent] Accession numbers: 70786. biodb.TRACE[2024-07-06 16:03:02.297][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:02.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:02.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.299][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:02.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:02.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:02.304][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:02.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:02.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:02.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:02.307][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:02.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:02.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:02.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:02.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:02.315][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:02.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:02.316][private$loadEntries] Creating entries from ids [1]: "78144". biodb.DEBUG[2024-07-06 16:03:02.317][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:02.319][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78144". biodb.TRACE[2024-07-06 16:03:02.320][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:02.321][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:02.322][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:02.323][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:02.324][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:02.324][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:02.327][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:02.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:02.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:02.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:02.333][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:02.334][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:02.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:02.336][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78144". biodb.DEBUG[2024-07-06 16:03:02.338][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:02.339][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:02.340][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78144". biodb.TRACE[2024-07-06 16:03:02.726][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78144). biodb.DEBUG[2024-07-06 16:03:03.116][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:03.118][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ede5a640bd42c7611e16282ef185b74.content" biodb.TRACE[2024-07-06 16:03:03.121][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ede5a640bd42c7611e16282ef185b74.request" biodb.TRACE[2024-07-06 16:03:03.123][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78144.xml" biodb.DEBUG[2024-07-06 16:03:03.124][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:03.125][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:03.126][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:03.128][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:03.128][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:03.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:03.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:03.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:03.135][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:03.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:03.137][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:03.138][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:03.139][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.140][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:03.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:03.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.145][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:03.146][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:03.146][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.147][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.148][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:03.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:03.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.152][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:03.153][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:03.154][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.154][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.156][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:03.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:03.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.159][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:03.160][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:03.161][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.162][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.163][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:03.164][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:03.165][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.165][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.166][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:03.167][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:03.168][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.169][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.170][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:03.171][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:03.172][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.173][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.174][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:03.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:03.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.177][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:03.178][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:03.179][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.180][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:03.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:03.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.185][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:03.186][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:03.187][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.188][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:03.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:03.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.192][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:03.193][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:03.194][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.195][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.196][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:03.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:03.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.200][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:03.201][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:03.202][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.202][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.203][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:03.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:03.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.223][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:03.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:03.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:03.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:03.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:03.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:03.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:03.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:03.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:03.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:03.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.244][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:03.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:03.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.248][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:03.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:03.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:03.251][self$createEntryFromContent] Accession numbers: 78144. biodb.TRACE[2024-07-06 16:03:03.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:03.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:03.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.256][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:03.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:03.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:03.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:03.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:03.263][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:03.264][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:03.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:03.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:03.270][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:03.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:03.271][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:03.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:03.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.277][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.280][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:03.281][private$selectFields] biodb.TRACE[2024-07-06 16:03:03.282][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:03.283][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:03.284][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:03.285][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.285][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.286][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.287][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.288][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.289][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.290][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.291][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.292][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:03.292][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:03.293][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.294][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.295][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.296][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.297][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:03.298][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.305][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.309][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-07-06 16:03:03.310][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:03.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:03.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:03.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:03.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:03.317][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:03.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:03.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.326][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:03.327][private$selectFields] biodb.TRACE[2024-07-06 16:03:03.328][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:03.329][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:03.329][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:03.330][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.331][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.332][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.333][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.334][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.335][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.336][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.337][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.338][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:03.339][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:03.339][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.340][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.341][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.342][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.343][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:03.344][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.348][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.355][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [28243]. biodb.DEBUG[2024-07-06 16:03:03.356][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:03.357][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:03.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:03.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:03.368][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:03.369][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:03.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:03.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.378][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:03.379][private$selectFields] biodb.TRACE[2024-07-06 16:03:03.380][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:03.381][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:03.381][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:03.382][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.383][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.384][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.385][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.386][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.387][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.388][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.388][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.389][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:03.390][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:03.391][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.392][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.393][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.394][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.394][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:03.395][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:03.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:03.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:03.406][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [78144]. biodb.DEBUG[2024-07-06 16:03:03.407][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:03.408][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:03.410][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:03.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:03.411][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:03.415][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:03.416][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:03.417][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:03.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:03.420][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.6*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:03.423][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:03.424][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:03.426][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.6%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:03:03.816][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.6%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:03:04.288][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:04.290][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9a13652ab89a613a3b0e10d3b6cb10a0.content" biodb.TRACE[2024-07-06 16:03:04.293][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9a13652ab89a613a3b0e10d3b6cb10a0.request" biodb.DEBUG[2024-07-06 16:03:04.297][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:04.298][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:04.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:04.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:04.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:04.304][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:04.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:04.306][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.313][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:04.316][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:04.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:04.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:04.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:04.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:04.323][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:04.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:04.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:04.336][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:04.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:04.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:04.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:04.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:04.343][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:04.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:04.345][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:04.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:04.356][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:04.358][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:04.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:04.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:04.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:04.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:04.365][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:04.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:04.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.383][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:04.384][private$selectFields] biodb.TRACE[2024-07-06 16:03:04.385][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:04.385][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:04.386][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:04.387][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.388][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.389][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.390][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.391][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.392][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.393][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.393][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.394][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:04.395][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:04.396][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.397][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.398][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.399][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.400][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:04.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.407][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.408][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.411][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-07-06 16:03:04.412][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:04.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:04.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:04.418][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:04.419][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:04.420][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:04.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:04.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.428][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:04.429][private$selectFields] biodb.TRACE[2024-07-06 16:03:04.430][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:04.431][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:04.432][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:04.433][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.434][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.434][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.435][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.436][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.437][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.438][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.439][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.440][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:04.440][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:04.441][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.442][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.443][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.444][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.445][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:04.446][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.449][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.455][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.457][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-07-06 16:03:04.458][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:04.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:04.459][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:04.463][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:04.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:04.465][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:04.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:04.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.473][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.474][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:04.475][private$selectFields] biodb.TRACE[2024-07-06 16:03:04.475][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:04.476][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:04.477][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:04.478][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.479][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.480][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.481][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.482][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.483][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.483][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.484][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.485][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:04.486][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:04.487][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.488][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.489][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.490][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.490][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:04.491][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.494][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.499][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:04.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:04.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:04.503][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [19804]. biodb.DEBUG[2024-07-06 16:03:04.504][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:04.504][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:04.506][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:04.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:04.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:04.512][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:04.513][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:04.514][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:04.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:04.517][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.3*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:04.520][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:04.526][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:04.528][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.3%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:03:04.917][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.3%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:03:05.311][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:05.313][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a985300ab8a01d49254fbf993ad91279.content" biodb.TRACE[2024-07-06 16:03:05.317][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a985300ab8a01d49254fbf993ad91279.request" biodb.DEBUG[2024-07-06 16:03:05.320][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:05.321][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:05.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:05.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:05.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:05.327][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:05.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:05.329][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:05.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:05.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:05.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:05.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:05.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:05.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:05.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:05.336][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:05.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:05.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:05.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:05.339][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:05.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:05.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:05.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:05.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:05.346][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:05.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:05.348][private$loadEntries] Creating entries from ids [1]: "47739". biodb.DEBUG[2024-07-06 16:03:05.349][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:05.351][cch$loadFileContent] Trying to load 1 files from cache: [1]: "47739". biodb.TRACE[2024-07-06 16:03:05.352][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:05.353][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:05.354][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:05.354][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:05.355][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:05.356][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:05.359][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:05.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:05.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:05.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:05.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:05.366][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:05.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:05.368][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=47739". biodb.DEBUG[2024-07-06 16:03:05.370][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:05.371][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:05.372][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=47739". biodb.TRACE[2024-07-06 16:03:05.763][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=47739). biodb.DEBUG[2024-07-06 16:03:06.150][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:06.152][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0dc9c92acc9df5971b3177a6daad90f3.content" biodb.TRACE[2024-07-06 16:03:06.155][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0dc9c92acc9df5971b3177a6daad90f3.request" biodb.TRACE[2024-07-06 16:03:06.157][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/47739.xml" biodb.DEBUG[2024-07-06 16:03:06.158][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:06.159][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:06.160][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:06.162][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:06.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:06.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:06.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:06.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:06.169][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:06.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:06.172][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:06.173][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:06.173][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.174][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:06.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:06.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.179][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:06.180][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:06.181][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.181][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.183][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:06.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:06.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.186][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:06.187][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:06.188][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.189][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.190][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:06.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:06.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.194][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:06.194][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:06.195][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.196][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.197][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:06.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:06.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.200][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.201][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:06.202][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:06.203][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.204][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.205][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:06.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:06.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.208][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:06.209][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:06.210][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.211][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.212][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:06.213][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:06.214][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.215][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.216][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:06.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:06.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.219][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:06.220][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:06.221][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.222][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.223][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:06.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:06.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.231][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:06.238][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:06.239][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.240][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.241][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:06.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:06.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.245][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:06.246][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:06.247][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.248][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.249][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:06.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:06.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.252][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:06.253][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:06.254][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.255][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.256][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:06.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:06.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.260][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:06.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:06.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:06.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:06.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.267][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:06.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:06.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:06.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:06.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:06.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:06.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:06.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:06.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:06.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:06.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:06.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:06.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:06.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:06.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:06.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:06.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:06.295][self$createEntryFromContent] Accession numbers: 47739. biodb.TRACE[2024-07-06 16:03:06.296][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:06.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:06.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:06.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:06.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:06.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:06.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:06.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:06.305][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:06.306][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:06.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:06.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:06.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:06.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:06.313][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:06.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:06.315][private$loadEntries] Creating entries from ids [1]: "51744". biodb.DEBUG[2024-07-06 16:03:06.316][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:06.318][cch$loadFileContent] Trying to load 1 files from cache: [1]: "51744". biodb.TRACE[2024-07-06 16:03:06.319][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:06.320][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:06.321][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:06.321][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:06.322][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:06.323][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:06.326][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:06.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:06.327][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:06.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:06.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:06.333][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:06.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:06.334][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51744". biodb.DEBUG[2024-07-06 16:03:06.337][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:06.338][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:06.339][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51744". biodb.TRACE[2024-07-06 16:03:06.725][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=51744). biodb.DEBUG[2024-07-06 16:03:07.112][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:07.116][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/34d89a621633962f5a6b9b09f1ef84ed.content" biodb.TRACE[2024-07-06 16:03:07.123][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/34d89a621633962f5a6b9b09f1ef84ed.request" biodb.TRACE[2024-07-06 16:03:07.128][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/51744.xml" biodb.DEBUG[2024-07-06 16:03:07.131][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:07.134][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:07.136][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:07.139][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:07.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:07.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:07.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:07.154][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:07.156][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:07.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:07.162][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:07.164][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:07.165][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.167][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:07.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:07.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.175][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:07.176][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:07.177][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.179][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.180][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:07.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:07.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.185][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:07.186][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:07.188][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.189][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.199][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:07.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:07.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.203][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:07.204][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:07.205][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.206][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.207][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:07.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:07.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.211][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:07.212][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:07.213][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.214][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.215][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:07.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:07.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.217][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.218][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:07.219][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:07.220][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.221][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.222][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:07.223][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:07.224][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.225][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.226][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:07.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:07.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.229][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:07.230][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:07.231][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.232][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.233][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:07.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:07.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.237][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:07.238][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:07.238][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.239][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.240][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:07.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:07.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.244][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:07.245][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:07.246][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.247][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.248][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:07.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:07.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.251][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:07.252][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:07.253][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.254][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.255][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:07.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:07.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:07.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:07.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.262][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:07.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:07.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:07.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:07.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.269][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:07.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:07.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:07.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:07.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:07.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:07.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.278][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:07.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:07.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:07.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:07.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:07.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:07.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:07.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:07.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:07.293][self$createEntryFromContent] Accession numbers: 51744. biodb.TRACE[2024-07-06 16:03:07.294][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:07.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:07.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.297][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.298][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:07.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:07.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:07.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:07.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:07.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:07.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:07.305][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:07.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:07.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:07.311][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:07.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:07.312][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:07.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:07.314][private$loadEntries] Creating entries from ids [1]: "64473". biodb.DEBUG[2024-07-06 16:03:07.315][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:07.316][cch$loadFileContent] Trying to load 1 files from cache: [1]: "64473". biodb.TRACE[2024-07-06 16:03:07.318][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:07.319][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:07.320][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:07.320][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:07.321][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:07.322][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:07.325][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:07.326][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:07.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:07.330][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:07.331][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:07.332][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:07.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:07.334][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64473". biodb.DEBUG[2024-07-06 16:03:07.337][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:07.337][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:07.339][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64473". biodb.TRACE[2024-07-06 16:03:07.753][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=64473). biodb.DEBUG[2024-07-06 16:03:08.172][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:08.190][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0bc75e6e381d0b772364b3d17c4c0f5e.content" biodb.TRACE[2024-07-06 16:03:08.197][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0bc75e6e381d0b772364b3d17c4c0f5e.request" biodb.TRACE[2024-07-06 16:03:08.202][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64473.xml" biodb.DEBUG[2024-07-06 16:03:08.205][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:08.208][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:08.211][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:08.214][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:08.216][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:08.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:08.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:08.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:08.227][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:08.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:08.232][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:08.234][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:08.235][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.236][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:08.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:08.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.243][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:08.244][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:08.245][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.246][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.248][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:08.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:08.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.252][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:08.253][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:08.254][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.255][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.257][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:08.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:08.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.261][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:08.262][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:08.262][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.263][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.264][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:08.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:08.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.268][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:08.269][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:08.270][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.271][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.272][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:08.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:08.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.275][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:08.276][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:08.277][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.278][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.279][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:08.280][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:08.281][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.282][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.283][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:08.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:08.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.286][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:08.287][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:08.288][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.289][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:08.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:08.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.293][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:08.294][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:08.295][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.296][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.297][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:08.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:08.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.301][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:08.302][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:08.303][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.303][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.304][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:08.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:08.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.308][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:08.309][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:08.310][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.311][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.312][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:08.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:08.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:08.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:08.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:08.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:08.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:08.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:08.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:08.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:08.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:08.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:08.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:08.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:08.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.336][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:08.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:08.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:08.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:08.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.343][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:08.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:08.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:08.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:08.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:08.351][self$createEntryFromContent] Accession numbers: 64473. biodb.TRACE[2024-07-06 16:03:08.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:08.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:08.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.355][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:08.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:08.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:08.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:08.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:08.368][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:08.368][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:08.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:08.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:08.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:08.375][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:08.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:08.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:08.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:08.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:08.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:08.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:08.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:08.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:08.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:08.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:08.388][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:08.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:08.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:08.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:08.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:08.394][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:08.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:08.396][private$loadEntries] Creating entries from ids [1]: "75244". biodb.DEBUG[2024-07-06 16:03:08.397][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:08.399][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75244". biodb.TRACE[2024-07-06 16:03:08.400][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:08.401][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:08.402][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:08.402][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:08.403][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:08.404][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:08.407][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:08.407][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:08.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:08.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:08.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:08.413][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:08.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:08.415][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75244". biodb.DEBUG[2024-07-06 16:03:08.418][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:08.419][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:08.420][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75244". biodb.TRACE[2024-07-06 16:03:08.827][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75244). biodb.DEBUG[2024-07-06 16:03:09.251][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:09.255][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cae81bf9939177869251c540dee6df85.content" biodb.TRACE[2024-07-06 16:03:09.262][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cae81bf9939177869251c540dee6df85.request" biodb.TRACE[2024-07-06 16:03:09.267][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75244.xml" biodb.DEBUG[2024-07-06 16:03:09.270][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:09.272][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:09.275][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:09.278][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:09.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:09.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:09.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:09.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:09.294][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:09.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:09.300][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:09.302][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:09.303][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.305][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:09.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:09.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.313][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:09.314][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:09.316][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.317][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.318][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:09.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:09.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.323][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:09.325][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:09.326][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.327][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.328][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:09.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:09.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.332][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:09.333][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:09.334][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.335][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.337][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:09.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:09.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.341][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:09.342][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:09.342][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.343][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:09.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:09.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.348][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:09.349][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:09.350][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.351][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.352][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:09.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:09.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.356][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:09.356][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:09.357][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.358][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.359][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:09.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:09.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.363][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:09.364][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:09.365][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.366][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.367][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:09.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:09.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.370][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:09.371][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:09.372][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.373][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.374][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:09.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:09.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.383][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:09.387][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:09.388][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.389][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.390][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:09.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:09.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.393][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.394][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:09.395][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:09.396][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.397][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.398][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:09.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:09.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.401][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.401][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:09.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:09.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:09.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:09.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.409][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:09.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:09.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.412][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:09.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:09.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:09.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:09.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:09.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:09.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:09.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:09.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.425][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:09.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:09.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.430][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:09.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:09.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.432][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.433][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:09.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:09.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:09.437][self$createEntryFromContent] Accession numbers: 75244. biodb.TRACE[2024-07-06 16:03:09.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:09.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:09.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:09.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:09.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:09.445][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:09.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:09.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:09.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:09.448][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:09.449][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:09.450][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:09.454][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:09.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:09.455][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:09.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:09.457][private$loadEntries] Creating entries from ids [1]: "75311". biodb.DEBUG[2024-07-06 16:03:09.458][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:09.459][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75311". biodb.TRACE[2024-07-06 16:03:09.460][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:09.461][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:09.462][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:09.463][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:09.464][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:09.465][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:09.467][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:09.468][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:09.469][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:09.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:09.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:09.475][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:09.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:09.476][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75311". biodb.DEBUG[2024-07-06 16:03:09.479][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:09.480][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:09.481][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75311". biodb.TRACE[2024-07-06 16:03:09.881][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75311). biodb.DEBUG[2024-07-06 16:03:10.314][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:10.318][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4e5c0f0d646c796bdaff17cc90a3658d.content" biodb.TRACE[2024-07-06 16:03:10.325][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4e5c0f0d646c796bdaff17cc90a3658d.request" biodb.TRACE[2024-07-06 16:03:10.330][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75311.xml" biodb.DEBUG[2024-07-06 16:03:10.333][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:10.336][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:10.338][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:10.341][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:10.343][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:10.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:10.354][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:10.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:10.358][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:10.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:10.363][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:10.365][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:10.366][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.368][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:10.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:10.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.376][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:10.377][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:10.378][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.380][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.381][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:10.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:10.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.386][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:10.387][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:10.389][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.390][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.391][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:10.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:10.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.395][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:10.396][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:10.397][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.407][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.408][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:10.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:10.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.412][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:10.413][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:10.414][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.415][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.416][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:10.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:10.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.419][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:10.420][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:10.421][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.422][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.423][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:10.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:10.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.427][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:10.428][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:10.428][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.429][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.430][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:10.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:10.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.434][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:10.435][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:10.436][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.436][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.438][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:10.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:10.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.441][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:10.442][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:10.443][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.444][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:10.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:10.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.448][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:10.449][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:10.450][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.451][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.452][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:10.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:10.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.455][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.456][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:10.457][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:10.457][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.458][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.459][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:10.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:10.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.462][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:10.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:10.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:10.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:10.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:10.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:10.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.473][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:10.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:10.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:10.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:10.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.480][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:10.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:10.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:10.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:10.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.486][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:10.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:10.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:10.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:10.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:10.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:10.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:10.498][self$createEntryFromContent] Accession numbers: 75311. biodb.TRACE[2024-07-06 16:03:10.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:10.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:10.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.502][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:10.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:10.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.505][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:10.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:10.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:10.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:10.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:10.509][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:10.510][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:10.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:10.515][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:10.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:10.517][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:10.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:10.518][private$loadEntries] Creating entries from ids [1]: "75350". biodb.DEBUG[2024-07-06 16:03:10.519][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:10.521][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75350". biodb.TRACE[2024-07-06 16:03:10.522][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:10.523][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:10.524][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:10.525][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:10.526][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:10.527][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:10.529][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:10.530][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:10.531][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:10.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:10.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:10.537][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:10.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:10.538][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75350". biodb.DEBUG[2024-07-06 16:03:10.541][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:10.542][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:10.543][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75350". biodb.TRACE[2024-07-06 16:03:10.942][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75350). biodb.DEBUG[2024-07-06 16:03:11.368][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:11.373][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/37625fe42e340de84bdcc226ef73c285.content" biodb.TRACE[2024-07-06 16:03:11.393][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/37625fe42e340de84bdcc226ef73c285.request" biodb.TRACE[2024-07-06 16:03:11.399][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75350.xml" biodb.DEBUG[2024-07-06 16:03:11.402][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:11.404][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:11.407][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:11.410][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:11.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:11.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:11.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:11.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:11.424][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:11.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:11.428][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:11.430][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:11.431][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.432][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:11.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:11.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.439][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:11.440][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:11.441][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.443][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.444][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:11.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:11.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.448][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:11.450][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:11.450][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.451][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.453][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:11.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:11.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.457][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:11.458][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:11.459][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.460][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.461][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:11.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:11.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.464][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:11.465][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:11.466][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.467][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.468][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:11.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:11.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.472][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:11.473][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:11.473][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.474][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.475][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:11.476][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:11.477][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.478][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.479][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:11.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:11.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.482][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:11.483][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:11.484][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.485][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:11.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:11.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.490][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:11.491][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:11.491][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.492][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:11.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:11.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.497][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:11.498][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:11.499][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.500][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.501][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:11.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:11.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.504][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:11.505][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:11.506][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.507][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.508][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:11.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:11.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.511][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:11.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:11.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:11.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:11.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:11.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:11.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:11.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:11.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:11.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:11.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.528][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:11.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:11.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:11.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:11.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:11.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:11.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:11.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:11.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.544][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:11.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:11.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:11.547][self$createEntryFromContent] Accession numbers: 75350. biodb.TRACE[2024-07-06 16:03:11.548][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:11.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:11.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:11.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:11.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:11.555][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:11.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:11.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:11.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:11.564][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:11.565][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:11.566][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:11.570][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:11.571][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:11.572][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:11.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:11.573][private$loadEntries] Creating entries from ids [1]: "87236". biodb.DEBUG[2024-07-06 16:03:11.574][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:11.576][cch$loadFileContent] Trying to load 1 files from cache: [1]: "87236". biodb.TRACE[2024-07-06 16:03:11.577][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:11.578][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:11.579][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:11.580][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:11.581][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:11.581][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:11.584][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:11.584][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:11.585][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:11.589][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:11.590][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:11.591][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:11.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:11.593][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=87236". biodb.DEBUG[2024-07-06 16:03:11.595][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:11.596][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:11.597][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=87236". biodb.TRACE[2024-07-06 16:03:11.998][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=87236). biodb.DEBUG[2024-07-06 16:03:12.393][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:12.395][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/668dc6e1fe28fb2b9645ffb56917cb44.content" biodb.TRACE[2024-07-06 16:03:12.398][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/668dc6e1fe28fb2b9645ffb56917cb44.request" biodb.TRACE[2024-07-06 16:03:12.400][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/87236.xml" biodb.DEBUG[2024-07-06 16:03:12.401][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:12.402][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:12.403][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:12.405][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:12.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:12.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:12.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:12.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:12.412][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:12.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:12.415][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:12.416][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:12.417][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.418][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:12.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:12.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.421][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.422][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:12.423][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:12.424][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.425][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.426][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:12.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:12.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.429][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:12.430][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:12.431][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.432][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.433][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:12.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:12.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.437][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:12.438][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:12.438][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.439][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.440][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:12.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:12.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.444][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:12.445][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:12.446][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.446][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.448][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:12.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:12.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.451][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:12.452][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:12.453][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.454][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.455][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:12.456][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:12.457][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.457][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.458][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:12.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:12.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.462][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:12.463][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:12.464][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.465][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.466][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:12.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:12.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.469][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:12.470][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:12.471][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.472][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:12.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:12.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.477][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:12.478][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:12.479][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.479][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.481][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:12.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:12.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.484][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:12.485][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:12.486][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.487][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.488][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:12.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:12.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.491][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:12.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:12.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.494][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.495][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:12.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:12.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.499][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:12.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:12.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:12.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:12.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.515][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:12.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:12.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.518][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:12.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:12.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:12.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:12.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:12.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:12.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.528][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:12.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:12.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:12.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:12.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:12.536][self$createEntryFromContent] Accession numbers: 87236. biodb.TRACE[2024-07-06 16:03:12.537][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:12.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:12.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:12.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:12.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:12.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:12.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:12.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:12.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:12.548][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:12.548][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:12.549][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:12.553][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:12.554][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:12.555][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:12.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:12.557][private$loadEntries] Creating entries from ids [1]: "132193". biodb.DEBUG[2024-07-06 16:03:12.557][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:12.559][cch$loadFileContent] Trying to load 1 files from cache: [1]: "132193". biodb.TRACE[2024-07-06 16:03:12.560][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:12.561][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:12.562][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:12.563][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:12.564][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:12.565][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:12.567][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:12.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:12.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:12.572][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:12.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:12.574][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:12.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:12.576][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132193". biodb.DEBUG[2024-07-06 16:03:12.578][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:12.579][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:12.580][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132193". biodb.TRACE[2024-07-06 16:03:12.979][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132193). biodb.DEBUG[2024-07-06 16:03:13.413][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:13.417][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/485d54e768e8b3a26016a2841d39a83c.content" biodb.TRACE[2024-07-06 16:03:13.424][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/485d54e768e8b3a26016a2841d39a83c.request" biodb.TRACE[2024-07-06 16:03:13.429][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/132193.xml" biodb.DEBUG[2024-07-06 16:03:13.432][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:13.435][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:13.437][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:13.440][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:13.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:13.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:13.453][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:13.455][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:13.457][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:13.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:13.462][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:13.464][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:13.465][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.467][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:13.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:13.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.473][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.475][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:13.476][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:13.477][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.479][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.480][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:13.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:13.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.485][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:13.486][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:13.487][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.489][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.490][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:13.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:13.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.494][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:13.495][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:13.496][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.497][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.499][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:13.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:13.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.502][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.503][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:13.504][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:13.504][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.505][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.506][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:13.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:13.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.510][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:13.511][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:13.512][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.513][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.514][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:13.515][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:13.516][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.517][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.518][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:13.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:13.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.529][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:13.531][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:13.532][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.533][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:13.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:13.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.537][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:13.538][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:13.539][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.540][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.541][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:13.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:13.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.545][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:13.546][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:13.547][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.548][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.549][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:13.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:13.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.552][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:13.553][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:13.554][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.555][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.556][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:13.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:13.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.560][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:13.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:13.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.563][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:13.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:13.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.567][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:13.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:13.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:13.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:13.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:13.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:13.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.578][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:13.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:13.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.581][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:13.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:13.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:13.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:13.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:13.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:13.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.592][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:13.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:13.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:13.595][self$createEntryFromContent] Accession numbers: 132193. biodb.TRACE[2024-07-06 16:03:13.596][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:13.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:13.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:13.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:13.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:13.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:13.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:13.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:13.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:13.607][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:13.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:13.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:13.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:13.613][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:13.614][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:13.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:13.616][private$loadEntries] Creating entries from ids [1]: "146002". biodb.DEBUG[2024-07-06 16:03:13.617][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:13.618][cch$loadFileContent] Trying to load 1 files from cache: [1]: "146002". biodb.TRACE[2024-07-06 16:03:13.620][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:13.621][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:13.621][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:13.622][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:13.623][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:13.624][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:13.627][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:13.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:13.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:13.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:13.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:13.634][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:13.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:13.636][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=146002". biodb.DEBUG[2024-07-06 16:03:13.638][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:13.639][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:13.641][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=146002". biodb.TRACE[2024-07-06 16:03:14.044][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=146002). biodb.DEBUG[2024-07-06 16:03:14.483][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:14.487][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f6f6aad2df3f38cd332b2e82fd62eca2.content" biodb.TRACE[2024-07-06 16:03:14.494][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f6f6aad2df3f38cd332b2e82fd62eca2.request" biodb.TRACE[2024-07-06 16:03:14.499][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/146002.xml" biodb.DEBUG[2024-07-06 16:03:14.502][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:14.504][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:14.507][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:14.510][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:14.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:14.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:14.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:14.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:14.527][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:14.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:14.532][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:14.534][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:14.536][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.537][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:14.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:14.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.545][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:14.556][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:14.557][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.559][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.560][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:14.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:14.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.564][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.565][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:14.566][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:14.567][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.568][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.569][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:14.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:14.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.573][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:14.574][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:14.575][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.576][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.577][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:14.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:14.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.581][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:14.581][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:14.582][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.583][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.584][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:14.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:14.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.588][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:14.589][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:14.590][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.590][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.591][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:14.592][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:14.593][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.594][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.595][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:14.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:14.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.599][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:14.600][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:14.601][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.601][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.602][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:14.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:14.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.606][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:14.607][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:14.608][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.609][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.610][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:14.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:14.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.613][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:14.614][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:14.615][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.616][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.617][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:14.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:14.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.621][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:14.621][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:14.622][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.623][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.624][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:14.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:14.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:14.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:14.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:14.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:14.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.635][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:14.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:14.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.637][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:14.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:14.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:14.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:14.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:14.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:14.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:14.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:14.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:14.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:14.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.655][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:14.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:14.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:14.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:14.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:14.663][self$createEntryFromContent] Accession numbers: 146002. biodb.TRACE[2024-07-06 16:03:14.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:14.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:14.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:14.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:14.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:14.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:14.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:14.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:14.674][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:14.675][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:14.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:14.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:14.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:14.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:14.682][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:14.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:14.684][private$loadEntries] Creating entries from ids [1]: "65641". biodb.DEBUG[2024-07-06 16:03:14.685][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:14.686][cch$loadFileContent] Trying to load 1 files from cache: [1]: "65641". biodb.TRACE[2024-07-06 16:03:14.687][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:14.688][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:14.689][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:14.690][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:14.691][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:14.692][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:14.694][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:14.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:14.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:14.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:14.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:14.706][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:14.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:14.709][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65641". biodb.DEBUG[2024-07-06 16:03:14.711][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:14.712][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:14.713][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65641". biodb.TRACE[2024-07-06 16:03:15.124][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65641). biodb.DEBUG[2024-07-06 16:03:15.551][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:15.555][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cb3af00d6d6a96efc61a93d5105272fc.content" biodb.TRACE[2024-07-06 16:03:15.562][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cb3af00d6d6a96efc61a93d5105272fc.request" biodb.TRACE[2024-07-06 16:03:15.567][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65641.xml" biodb.DEBUG[2024-07-06 16:03:15.570][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:15.572][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:15.575][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:15.578][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:15.580][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:15.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:15.591][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:15.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:15.595][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:15.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:15.601][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:15.602][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:15.604][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.605][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.607][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:15.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:15.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.613][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:15.615][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:15.616][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.617][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.619][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:15.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:15.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.623][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.624][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:15.625][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:15.626][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.627][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.629][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:15.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:15.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.633][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:15.634][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:15.635][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.636][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.637][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:15.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:15.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.641][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:15.642][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:15.643][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.644][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.645][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:15.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:15.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.649][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:15.650][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:15.651][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.651][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.653][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:15.653][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:15.654][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.655][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.656][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:15.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:15.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.659][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.660][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:15.661][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:15.662][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.662][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:15.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:15.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.667][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:15.668][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:15.669][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.670][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.671][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:15.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:15.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.674][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:15.675][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:15.676][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.677][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.678][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:15.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:15.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.682][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:15.682][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:15.683][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.684][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.685][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:15.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:15.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.689][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:15.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:15.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.692][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:15.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:15.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.695][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:15.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:15.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.700][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:15.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:15.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.703][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:15.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:15.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:15.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:15.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.709][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:15.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:15.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:15.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:15.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:15.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:15.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:15.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:15.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.732][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:15.733][self$createEntryFromContent] Accession numbers: 65641. biodb.TRACE[2024-07-06 16:03:15.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:15.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:15.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:15.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:15.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:15.742][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:15.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:15.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:15.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:15.745][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:15.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:15.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:15.751][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:15.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:15.752][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:15.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:15.754][private$loadEntries] Creating entries from ids [1]: "144071". biodb.DEBUG[2024-07-06 16:03:15.755][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:15.756][cch$loadFileContent] Trying to load 1 files from cache: [1]: "144071". biodb.TRACE[2024-07-06 16:03:15.757][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:15.758][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:15.759][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:15.760][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:15.761][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:15.762][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:15.764][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:15.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:15.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:15.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:15.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:15.771][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:15.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:15.773][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=144071". biodb.DEBUG[2024-07-06 16:03:15.776][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:15.776][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:15.778][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=144071". biodb.TRACE[2024-07-06 16:03:16.229][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=144071). biodb.DEBUG[2024-07-06 16:03:16.656][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:16.660][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/147c6b10a8e09e725fbbb250103f039d.content" biodb.TRACE[2024-07-06 16:03:16.667][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/147c6b10a8e09e725fbbb250103f039d.request" biodb.TRACE[2024-07-06 16:03:16.672][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/144071.xml" biodb.DEBUG[2024-07-06 16:03:16.675][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:16.678][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:16.681][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:16.684][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:16.686][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:16.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:16.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:16.698][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:16.700][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:16.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:16.705][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:16.707][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:16.709][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.710][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.712][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:16.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:16.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.718][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:16.720][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:16.721][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.722][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.724][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:16.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:16.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.729][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:16.730][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:16.731][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.732][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.733][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:16.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:16.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.738][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:16.739][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:16.740][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.741][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.742][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:16.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:16.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.746][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:16.747][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:16.748][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.749][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:16.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:16.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.753][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:16.754][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:16.755][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.756][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.757][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:16.758][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.759][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.760][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.761][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:16.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.765][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:16.766][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:16.766][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.767][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:16.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:16.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.772][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:16.773][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:16.774][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.775][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.776][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:16.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:16.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.780][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:16.780][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:16.781][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.782][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.783][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:16.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:16.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.798][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:16.799][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:16.800][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.801][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.802][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:16.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:16.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:16.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:16.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:16.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:16.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:16.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:16.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:16.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:16.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.820][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:16.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:16.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.824][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:16.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:16.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.828][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:16.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:16.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.831][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:16.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:16.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:16.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:16.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:16.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:16.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:16.842][self$createEntryFromContent] Accession numbers: 144071. biodb.TRACE[2024-07-06 16:03:16.843][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:16.854][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:16.854][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:16.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:16.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:16.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:16.861][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:16.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:16.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.866][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:16.873][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:16.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:16.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:16.879][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:16.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:16.880][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:16.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:16.882][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.885][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.889][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:16.892][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:16.893][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:16.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:16.898][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:16.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:16.899][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:16.900][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:16.901][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.905][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.908][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:16.912][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:16.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:16.913][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:16.917][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:16.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:16.919][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:16.920][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:16.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.924][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.924][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:16.932][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:16.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:16.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:16.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:16.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:16.939][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:16.939][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:16.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:16.957][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:16.958][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:16.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:16.963][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:16.964][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:16.965][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:16.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:16.966][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:16.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:16.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:16.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:16.977][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:16.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:16.978][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:16.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:16.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:16.984][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:16.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:16.986][private$loadEntries] Creating entries from ids [1]: "168650". biodb.DEBUG[2024-07-06 16:03:16.987][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:16.988][cch$loadFileContent] Trying to load 1 files from cache: [1]: "168650". biodb.TRACE[2024-07-06 16:03:16.989][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:16.990][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:16.991][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:16.992][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:16.993][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:16.994][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:16.996][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:16.997][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:16.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:17.002][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:17.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:17.003][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:17.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:17.005][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=168650". biodb.DEBUG[2024-07-06 16:03:17.008][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:17.008][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:17.010][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=168650". biodb.TRACE[2024-07-06 16:03:17.401][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=168650). biodb.DEBUG[2024-07-06 16:03:17.817][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:17.820][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/fbd7acd341e86313aeb547b3d6d3201b.content" biodb.TRACE[2024-07-06 16:03:17.825][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/fbd7acd341e86313aeb547b3d6d3201b.request" biodb.TRACE[2024-07-06 16:03:17.830][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/168650.xml" biodb.DEBUG[2024-07-06 16:03:17.832][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:17.834][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:17.836][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:17.838][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:17.840][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:17.841][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:17.849][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:17.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:17.852][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:17.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:17.857][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:17.859][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:17.861][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.862][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:17.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:17.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.869][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:17.871][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:17.872][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.873][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.875][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:17.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:17.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.880][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:17.881][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:17.882][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.883][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.885][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:17.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:17.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.889][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:17.890][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:17.891][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.892][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:17.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:17.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.896][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.897][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:17.898][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:17.899][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.900][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.901][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:17.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:17.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.905][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:17.906][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:17.907][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.908][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.909][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:17.910][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:17.911][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.912][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.913][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:17.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:17.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.917][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:17.918][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:17.919][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.919][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:17.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:17.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.924][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:17.925][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:17.926][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.935][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.936][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:17.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:17.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.941][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:17.942][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:17.943][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.943][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.944][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:17.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:17.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.948][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:17.949][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:17.950][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.951][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.952][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:17.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:17.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:17.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:17.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:17.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:17.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:17.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:17.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.966][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:17.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:17.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:17.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:17.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:17.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:17.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:17.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:17.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:17.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:17.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:17.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:17.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:17.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:17.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:17.991][self$createEntryFromContent] Accession numbers: 168650. biodb.TRACE[2024-07-06 16:03:17.992][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:17.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:17.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:17.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:17.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:17.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:17.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:17.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:18.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:18.002][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:18.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:18.004][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:18.008][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:18.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:18.009][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:18.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:18.011][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:18.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:18.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:18.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:18.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:18.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:18.018][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:18.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:18.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:18.021][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:18.022][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:18.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:18.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:18.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:18.029][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:18.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:18.030][private$loadEntries] Creating entries from ids [1]: "169305". biodb.DEBUG[2024-07-06 16:03:18.031][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:18.033][cch$loadFileContent] Trying to load 1 files from cache: [1]: "169305". biodb.TRACE[2024-07-06 16:03:18.034][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:18.035][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:18.036][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:18.037][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:18.037][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:18.038][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:18.041][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:18.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:18.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:18.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:18.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:18.048][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:18.049][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:18.050][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169305". biodb.DEBUG[2024-07-06 16:03:18.052][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:18.053][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:18.054][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169305". biodb.TRACE[2024-07-06 16:03:18.451][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=169305). biodb.DEBUG[2024-07-06 16:03:18.873][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:18.877][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5eab934e4cfb5514f373385a6170c282.content" biodb.TRACE[2024-07-06 16:03:18.884][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5eab934e4cfb5514f373385a6170c282.request" biodb.TRACE[2024-07-06 16:03:18.889][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/169305.xml" biodb.DEBUG[2024-07-06 16:03:18.892][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:18.895][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:18.897][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:18.901][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:18.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:18.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:18.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:18.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:18.917][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:18.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:18.933][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:18.935][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:18.937][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.938][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:18.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:18.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:18.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:18.945][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:18.947][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:18.948][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.949][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:18.950][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:18.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:18.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:18.955][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:18.956][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:18.957][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.958][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:18.959][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:18.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:18.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:18.963][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:18.964][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:18.965][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.966][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:18.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:18.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:18.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:18.971][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:18.972][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:18.972][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.973][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:18.974][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:18.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:18.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.977][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:18.978][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:18.979][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:18.980][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.981][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:18.982][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:18.983][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:18.984][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.984][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:18.985][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:18.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:18.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:18.989][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:18.990][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:18.991][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.992][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:18.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:18.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:18.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:18.996][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:18.997][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:18.998][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:18.999][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.000][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:19.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:19.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.004][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:19.005][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:19.006][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.006][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.007][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:19.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:19.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.011][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:19.012][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:19.013][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.014][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.015][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:19.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:19.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:19.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:19.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:19.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:19.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:19.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:19.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:19.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:19.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:19.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:19.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:19.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:19.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.039][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:19.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:19.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:19.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:19.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:19.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:19.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.049][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:19.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:19.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:19.054][self$createEntryFromContent] Accession numbers: 169305. biodb.TRACE[2024-07-06 16:03:19.055][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:19.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:19.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:19.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:19.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:19.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:19.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:19.066][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:19.067][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:19.068][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:19.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:19.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:19.073][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:19.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:19.075][private$loadEntries] Creating entries from ids [1]: "176869". biodb.DEBUG[2024-07-06 16:03:19.076][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:19.078][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176869". biodb.TRACE[2024-07-06 16:03:19.079][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:19.080][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:19.081][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:19.082][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:19.083][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:19.084][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:19.091][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:19.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:19.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:19.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:19.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:19.099][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:19.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:19.101][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176869". biodb.DEBUG[2024-07-06 16:03:19.104][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:19.105][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:19.106][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176869". biodb.TRACE[2024-07-06 16:03:19.503][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176869). biodb.DEBUG[2024-07-06 16:03:19.932][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:19.936][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2c477fa42863c662724815d047e8c32.content" biodb.TRACE[2024-07-06 16:03:19.943][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2c477fa42863c662724815d047e8c32.request" biodb.TRACE[2024-07-06 16:03:19.948][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176869.xml" biodb.DEBUG[2024-07-06 16:03:19.951][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:19.953][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:19.956][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:19.959][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:19.961][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:19.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:19.972][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:19.974][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:19.975][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:19.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:19.981][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:19.983][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:19.984][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.986][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:19.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:19.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.994][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:19.995][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:19.997][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:19.998][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:19.999][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:20.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:20.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.004][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:20.006][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:20.007][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.008][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.009][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:20.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:20.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.014][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:20.015][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:20.016][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.017][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.018][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:20.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:20.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.022][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:20.023][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:20.024][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.024][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.026][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:20.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:20.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.029][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:20.030][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:20.031][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.032][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.033][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:20.034][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:20.035][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.035][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.037][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:20.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:20.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.040][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:20.041][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:20.042][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.043][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:20.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:20.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.047][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:20.048][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:20.049][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.050][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.051][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:20.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:20.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.055][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:20.056][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:20.057][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.057][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.058][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:20.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:20.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.062][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:20.063][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:20.064][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.065][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.066][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:20.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:20.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:20.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:20.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:20.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:20.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:20.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:20.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:20.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:20.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:20.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:20.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:20.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:20.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.091][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:20.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:20.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:20.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:20.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:20.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:20.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:20.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:20.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:20.115][self$createEntryFromContent] Accession numbers: 176869. biodb.TRACE[2024-07-06 16:03:20.116][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:20.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:20.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.119][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:20.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:20.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:20.123][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:20.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:20.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:20.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:20.126][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:20.127][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:20.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:20.132][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:20.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:20.134][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:20.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:20.135][private$loadEntries] Creating entries from ids [1]: "185696". biodb.DEBUG[2024-07-06 16:03:20.136][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:20.138][cch$loadFileContent] Trying to load 1 files from cache: [1]: "185696". biodb.TRACE[2024-07-06 16:03:20.139][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:20.140][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:20.141][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:20.142][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:20.143][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:20.144][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:20.146][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:20.147][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:20.147][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:20.152][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:20.152][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:20.153][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:20.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:20.155][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=185696". biodb.DEBUG[2024-07-06 16:03:20.157][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:20.158][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:20.159][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=185696". biodb.TRACE[2024-07-06 16:03:20.565][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=185696). biodb.DEBUG[2024-07-06 16:03:20.999][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:21.003][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/030ac759c83231dbd7b7d6c83788888c.content" biodb.TRACE[2024-07-06 16:03:21.010][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/030ac759c83231dbd7b7d6c83788888c.request" biodb.TRACE[2024-07-06 16:03:21.015][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/185696.xml" biodb.DEBUG[2024-07-06 16:03:21.018][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:21.021][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:21.023][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:21.026][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:21.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:21.030][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:21.039][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:21.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:21.043][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:21.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:21.048][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:21.050][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:21.052][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.053][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:21.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:21.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.060][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.061][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:21.063][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:21.064][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.065][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.067][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:21.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:21.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.072][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:21.073][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:21.074][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.075][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.077][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:21.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:21.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.081][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:21.082][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:21.083][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.084][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:21.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:21.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.089][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:21.090][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:21.091][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.092][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.093][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:21.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:21.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.097][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:21.098][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:21.099][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.100][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.101][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:21.102][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:21.103][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.104][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.105][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:21.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:21.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.108][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:21.109][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:21.110][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.111][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:21.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:21.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.116][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:21.117][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:21.117][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.118][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.120][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:21.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:21.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.123][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:21.124][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:21.125][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.131][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.135][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:21.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:21.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.139][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:21.141][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:21.141][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.142][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.143][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:21.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:21.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.147][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:21.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:21.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:21.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:21.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:21.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:21.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.158][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:21.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:21.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.161][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:21.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:21.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.165][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:21.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:21.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:21.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:21.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:21.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:21.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.175][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:21.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:21.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.179][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:21.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:21.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:21.182][self$createEntryFromContent] Accession numbers: 185696. biodb.TRACE[2024-07-06 16:03:21.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:21.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:21.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:21.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:21.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:21.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:21.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:21.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:21.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:21.194][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:21.194][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:21.195][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:21.199][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:21.200][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:21.201][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:21.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:21.203][private$loadEntries] Creating entries from ids [1]: "190762". biodb.DEBUG[2024-07-06 16:03:21.203][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:21.205][cch$loadFileContent] Trying to load 1 files from cache: [1]: "190762". biodb.TRACE[2024-07-06 16:03:21.206][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:21.207][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:21.208][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:21.209][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:21.210][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:21.210][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:21.213][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:21.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:21.214][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:21.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:21.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:21.220][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:21.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:21.222][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=190762". biodb.DEBUG[2024-07-06 16:03:21.224][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:21.225][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:21.227][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=190762". biodb.TRACE[2024-07-06 16:03:21.627][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=190762). biodb.DEBUG[2024-07-06 16:03:22.057][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:22.061][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/fa9da4de7d7dc0d4458ab1ff7bbbbda0.content" biodb.TRACE[2024-07-06 16:03:22.068][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/fa9da4de7d7dc0d4458ab1ff7bbbbda0.request" biodb.TRACE[2024-07-06 16:03:22.073][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/190762.xml" biodb.DEBUG[2024-07-06 16:03:22.076][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:22.078][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:22.081][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:22.084][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:22.086][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:22.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:22.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:22.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:22.101][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:22.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:22.106][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:22.108][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:22.109][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.111][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:22.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:22.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.119][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:22.120][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:22.121][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.123][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.124][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:22.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:22.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.129][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:22.131][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:22.132][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.133][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.134][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:22.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:22.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.139][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:22.140][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:22.141][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.142][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.143][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:22.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:22.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.156][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:22.157][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:22.158][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.159][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.160][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:22.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:22.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.164][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:22.165][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:22.166][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.167][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.168][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:22.169][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:22.170][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.171][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.172][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:22.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:22.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.175][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:22.176][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:22.177][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.178][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:22.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:22.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.183][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:22.184][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:22.185][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.185][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.187][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:22.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:22.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.190][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:22.191][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:22.192][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.193][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.194][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:22.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:22.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.198][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:22.198][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:22.199][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.200][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.201][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:22.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:22.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:22.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:22.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:22.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:22.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:22.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:22.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:22.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:22.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.219][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:22.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:22.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:22.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:22.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:22.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:22.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:22.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:22.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:22.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:22.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.236][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:22.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:22.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.239][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:22.240][self$createEntryFromContent] Accession numbers: 190762. biodb.TRACE[2024-07-06 16:03:22.241][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:22.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:22.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.244][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:22.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:22.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:22.248][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:22.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:22.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:22.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:22.251][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:22.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:22.253][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:22.257][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:22.258][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:22.258][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:22.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:22.260][private$loadEntries] Creating entries from ids [1]: "193176". biodb.DEBUG[2024-07-06 16:03:22.261][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:22.262][cch$loadFileContent] Trying to load 1 files from cache: [1]: "193176". biodb.TRACE[2024-07-06 16:03:22.264][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:22.265][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:22.266][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:22.266][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:22.267][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:22.268][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:22.271][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:22.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:22.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:22.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:22.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:22.278][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:22.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:22.280][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=193176". biodb.DEBUG[2024-07-06 16:03:22.282][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:22.283][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:22.284][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=193176". biodb.TRACE[2024-07-06 16:03:22.684][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=193176). biodb.DEBUG[2024-07-06 16:03:23.117][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:23.121][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/343c078fd7b00f04bd71e6f2aebb6ed3.content" biodb.TRACE[2024-07-06 16:03:23.128][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/343c078fd7b00f04bd71e6f2aebb6ed3.request" biodb.TRACE[2024-07-06 16:03:23.133][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/193176.xml" biodb.DEBUG[2024-07-06 16:03:23.136][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:23.153][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:23.155][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:23.159][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:23.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:23.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:23.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:23.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:23.174][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:23.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:23.179][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:23.181][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:23.182][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.183][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:23.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:23.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.190][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:23.192][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:23.193][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.194][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.195][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:23.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:23.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.200][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:23.201][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:23.202][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.203][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.204][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:23.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:23.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.208][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:23.209][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:23.210][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.211][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.212][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:23.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:23.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.216][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:23.217][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:23.218][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.219][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.220][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:23.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:23.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.223][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:23.224][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:23.225][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.226][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.227][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:23.228][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:23.229][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.230][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.231][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:23.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:23.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.234][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:23.235][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:23.236][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.237][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:23.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:23.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.241][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:23.242][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:23.243][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.244][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.245][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:23.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:23.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.249][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:23.250][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:23.251][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.251][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.252][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:23.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:23.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.256][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:23.257][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:23.258][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.259][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.260][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:23.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:23.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:23.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:23.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:23.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:23.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.270][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:23.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:23.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:23.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:23.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.277][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:23.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:23.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:23.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:23.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.284][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:23.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:23.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:23.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:23.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:23.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:23.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:23.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:23.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:23.299][self$createEntryFromContent] Accession numbers: 193176. biodb.TRACE[2024-07-06 16:03:23.300][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:23.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:23.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:23.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:23.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:23.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:23.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:23.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:23.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:23.311][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:23.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:23.312][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:23.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:23.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:23.323][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:23.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:23.325][private$loadEntries] Creating entries from ids [1]: "196395". biodb.DEBUG[2024-07-06 16:03:23.326][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:23.328][cch$loadFileContent] Trying to load 1 files from cache: [1]: "196395". biodb.TRACE[2024-07-06 16:03:23.329][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:23.330][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:23.331][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:23.332][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:23.333][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:23.334][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:23.336][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:23.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:23.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:23.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:23.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:23.343][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:23.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:23.345][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=196395". biodb.DEBUG[2024-07-06 16:03:23.347][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:23.348][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:23.350][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=196395". biodb.TRACE[2024-07-06 16:03:23.831][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=196395). biodb.DEBUG[2024-07-06 16:03:24.258][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:24.262][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/73421bc681b7c5ac1a6297ef414ac513.content" biodb.TRACE[2024-07-06 16:03:24.269][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/73421bc681b7c5ac1a6297ef414ac513.request" biodb.TRACE[2024-07-06 16:03:24.274][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/196395.xml" biodb.DEBUG[2024-07-06 16:03:24.277][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:24.280][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:24.282][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:24.285][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.287][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.298][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.302][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:24.307][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:24.309][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:24.311][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.312][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:24.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:24.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.320][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:24.321][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:24.323][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.324][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.326][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:24.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:24.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.330][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:24.332][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:24.333][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.334][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.336][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:24.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:24.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.340][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:24.341][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:24.342][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.343][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.344][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:24.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:24.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.348][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:24.349][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:24.350][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.351][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:24.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:24.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.355][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:24.356][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:24.357][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.358][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.359][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:24.360][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.361][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.362][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.363][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:24.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.366][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:24.367][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:24.368][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.369][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:24.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:24.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.374][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:24.375][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:24.375][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.376][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.378][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:24.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:24.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.381][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:24.382][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:24.383][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.384][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.385][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:24.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:24.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.389][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:24.390][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:24.391][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.391][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.393][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:24.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:24.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:24.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:24.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.407][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.419][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:24.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:24.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:24.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:24.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:24.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:24.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.431][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:24.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:24.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:24.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:24.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.437][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.438][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:24.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:24.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:24.441][self$createEntryFromContent] Accession numbers: 196395. biodb.TRACE[2024-07-06 16:03:24.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:24.453][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.453][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.460][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:24.462][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.465][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.469][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:24.472][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:24.474][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.474][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.480][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.481][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:24.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.488][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.489][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.490][private$selectFields] biodb.TRACE[2024-07-06 16:03:24.491][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:24.492][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:24.493][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.494][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.494][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.495][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.496][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.497][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.498][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.499][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.500][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.500][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.501][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.502][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.503][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.504][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.505][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.506][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:24.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.517][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-07-06 16:03:24.518][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.526][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:24.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.535][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.535][private$selectFields] biodb.TRACE[2024-07-06 16:03:24.536][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:24.537][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:24.538][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.539][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.540][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.541][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.542][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.542][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.543][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.544][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.545][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.546][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.547][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.548][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.549][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.549][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.550][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.551][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:24.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.556][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.564][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.569][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [71954]. biodb.DEBUG[2024-07-06 16:03:24.570][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.572][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.576][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.577][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.577][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:24.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.582][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.586][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.587][private$selectFields] biodb.TRACE[2024-07-06 16:03:24.588][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:24.589][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:24.589][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.590][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.591][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.592][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.593][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.594][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.595][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.596][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.596][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.597][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.598][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.599][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.600][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.601][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.602][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.602][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:24.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.610][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.614][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [197612]. biodb.DEBUG[2024-07-06 16:03:24.615][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:24.616][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:24.632][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.637][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.639][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:24.642][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.5*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:24.645][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:03:24.646][cch$loadFileContent] Trying to load 1 files from cache: [1]: "ebf8c17fa19fb0caf99d83ca8441a2ac". biodb.TRACE[2024-07-06 16:03:24.647][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:03:24.648][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ebf8c17fa19fb0caf99d83ca8441a2ac.content". biodb.DEBUG[2024-07-06 16:03:24.653][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.653][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.654][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.658][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.659][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:24.661][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.664][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.671][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:24.672][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.679][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:24.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.688][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:24.691][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.697][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.698][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:24.700][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.716][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:24.717][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.718][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.719][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.723][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.725][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.725][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:24.726][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.729][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.732][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.733][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:24.737][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:24.738][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.744][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.745][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:24.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.751][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.754][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.755][private$selectFields] biodb.TRACE[2024-07-06 16:03:24.756][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:24.757][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:24.757][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.758][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.759][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.760][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.761][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.762][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.763][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.764][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.764][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.765][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.766][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.767][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.768][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.769][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.770][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.770][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:24.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.775][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.782][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [3014]. biodb.DEBUG[2024-07-06 16:03:24.783][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.790][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:24.792][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.796][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.799][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.800][private$selectFields] biodb.TRACE[2024-07-06 16:03:24.801][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:24.802][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:24.803][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.803][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.804][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.805][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.806][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.807][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.808][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.809][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.810][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.810][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.811][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.812][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.813][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.814][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.815][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.816][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:24.817][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.820][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.828][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [8021]. biodb.DEBUG[2024-07-06 16:03:24.829][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.830][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.834][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.835][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.836][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.837][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:24.838][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.842][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.845][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.846][private$selectFields] biodb.TRACE[2024-07-06 16:03:24.847][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:24.848][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:24.853][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.855][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.856][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.857][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.858][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.859][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.860][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.861][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.862][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.863][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.864][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:24.865][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.866][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.867][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.867][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.868][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:24.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.873][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.876][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:24.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.880][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [30382]. biodb.DEBUG[2024-07-06 16:03:24.881][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:24.882][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:24.884][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.891][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:24.894][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.4*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:24.897][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:03:24.898][cch$loadFileContent] Trying to load 1 files from cache: [1]: "152225e020c3e5947a0f5a90f021cee7". biodb.TRACE[2024-07-06 16:03:24.899][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:03:24.900][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/152225e020c3e5947a0f5a90f021cee7.content". biodb.DEBUG[2024-07-06 16:03:24.903][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.904][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.908][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.910][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:24.912][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.919][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:24.922][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.923][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.924][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.929][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:24.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:24.941][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.947][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.948][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:24.950][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.954][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.957][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:24.961][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.966][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.968][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:24.970][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.973][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.977][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:24.981][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:24.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:24.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:24.986][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:24.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:24.988][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:24.988][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:24.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:24.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:24.993][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:24.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:25.007][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.008][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.008][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.013][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.014][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.023][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:25.027][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.027][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.032][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.033][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.035][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.038][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.039][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.042][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:25.046][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:25.047][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.054][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.063][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.064][private$selectFields] biodb.TRACE[2024-07-06 16:03:25.065][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:25.065][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:25.066][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.067][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.068][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.069][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.070][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.071][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.072][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.072][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.073][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.074][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.075][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.076][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.077][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.078][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.078][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.079][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:25.080][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.083][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.084][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.090][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.091][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [65530]. biodb.DEBUG[2024-07-06 16:03:25.092][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.099][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.101][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.108][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.109][private$selectFields] biodb.TRACE[2024-07-06 16:03:25.110][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:25.111][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:25.112][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.113][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.113][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.114][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.115][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.116][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.117][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.118][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.119][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.120][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.121][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.121][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.122][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.123][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.124][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.125][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:25.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.137][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [90204]. biodb.DEBUG[2024-07-06 16:03:25.138][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.151][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.160][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.161][private$selectFields] biodb.TRACE[2024-07-06 16:03:25.162][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:25.163][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:25.164][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.164][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.165][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.166][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.167][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.168][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.169][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.170][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.170][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.171][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.172][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.173][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.174][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.175][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.176][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.177][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:25.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.181][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.188][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [132793]. biodb.DEBUG[2024-07-06 16:03:25.189][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:25.190][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:25.192][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.192][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.199][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:25.202][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:25.205][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:03:25.206][cch$loadFileContent] Trying to load 1 files from cache: [1]: "9686ce9c957a368dd8f5b4cc9c5b15b3". biodb.TRACE[2024-07-06 16:03:25.207][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:03:25.208][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9686ce9c957a368dd8f5b4cc9c5b15b3.content". biodb.DEBUG[2024-07-06 16:03:25.210][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.211][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.212][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.216][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.217][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.223][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:25.230][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.231][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.237][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.238][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.239][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.242][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.246][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:25.250][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.2*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:25.253][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:03:25.254][cch$loadFileContent] Trying to load 1 files from cache: [1]: "5d833e77a1be58060d0c3916a1e1b293". biodb.TRACE[2024-07-06 16:03:25.255][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:03:25.257][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5d833e77a1be58060d0c3916a1e1b293.content". biodb.DEBUG[2024-07-06 16:03:25.259][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.261][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.265][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.267][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.276][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.278][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:25.279][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.280][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.287][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.297][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.298][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.305][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:25.306][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.307][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.314][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.315][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.319][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.322][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:25.326][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:25.327][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.328][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.333][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.334][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.335][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.343][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.344][private$selectFields] biodb.TRACE[2024-07-06 16:03:25.345][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:25.346][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:25.347][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.348][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.349][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.349][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.350][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.351][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.352][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.353][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.354][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.355][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.356][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.356][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.357][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.358][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.359][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.360][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:25.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.372][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [51836]. biodb.DEBUG[2024-07-06 16:03:25.373][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.374][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.380][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.389][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.389][private$selectFields] biodb.TRACE[2024-07-06 16:03:25.390][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:25.391][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:25.392][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.393][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.394][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.395][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.395][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.396][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.397][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.398][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.399][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.400][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.401][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.402][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.402][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.403][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.404][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.405][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:25.406][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.409][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.412][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.416][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.417][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [51837]. biodb.DEBUG[2024-07-06 16:03:25.418][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.419][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.420][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.426][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.431][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.434][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.435][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.436][private$selectFields] biodb.TRACE[2024-07-06 16:03:25.441][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:25.442][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:25.444][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.445][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.446][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.447][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.448][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.449][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.450][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.451][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.451][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.452][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.453][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.454][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.455][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.456][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.457][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.458][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:25.459][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.469][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [132205]. biodb.DEBUG[2024-07-06 16:03:25.470][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:25.471][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:25.487][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.488][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.489][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.494][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.495][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:25.498][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:25.500][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:03:25.502][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-07-06 16:03:25.503][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:03:25.504][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-07-06 16:03:25.506][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.507][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.507][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.511][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.512][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.513][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.515][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.518][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.522][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:25.526][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:25.529][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:03:25.530][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-07-06 16:03:25.531][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:03:25.532][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-07-06 16:03:25.534][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.541][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.550][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:25.554][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.561][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.561][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:25.574][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:25.576][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.577][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.577][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.581][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.583][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.584][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.598][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.599][private$selectFields] biodb.TRACE[2024-07-06 16:03:25.600][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:25.601][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:25.602][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.602][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.603][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.604][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.605][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.606][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.607][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.608][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.609][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.610][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.610][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.611][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.612][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.613][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.614][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.615][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:25.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.626][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288]. biodb.DEBUG[2024-07-06 16:03:25.627][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.634][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.639][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.642][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.643][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.644][private$selectFields] biodb.TRACE[2024-07-06 16:03:25.645][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:25.646][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:25.647][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.647][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.648][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.649][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.650][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.651][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.652][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.653][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.654][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.654][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.655][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.656][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.657][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.658][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.659][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.660][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:25.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.663][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.667][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.671][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-07-06 16:03:25.672][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.678][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.679][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.681][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.685][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.688][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.689][private$selectFields] biodb.TRACE[2024-07-06 16:03:25.690][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:25.691][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:25.691][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.692][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.693][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.694][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.695][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.696][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.697][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.698][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.698][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.699][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.700][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.701][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.702][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.703][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.704][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.705][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:25.705][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.709][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.713][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.715][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.717][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892]. biodb.DEBUG[2024-07-06 16:03:25.718][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:25.718][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:25.720][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.721][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.722][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.726][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.727][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.727][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:25.736][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:25.739][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:03:25.741][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b3cd8ddf08f509014f10dc9bf7c1649d". biodb.TRACE[2024-07-06 16:03:25.742][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:03:25.743][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b3cd8ddf08f509014f10dc9bf7c1649d.content". biodb.DEBUG[2024-07-06 16:03:25.745][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.746][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.752][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.761][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:25.764][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.766][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.770][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.771][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.777][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.780][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:25.784][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:25.787][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:03:25.788][cch$loadFileContent] Trying to load 1 files from cache: [1]: "831507e33c6cf42061851262412f5feb". biodb.TRACE[2024-07-06 16:03:25.789][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:03:25.791][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/831507e33c6cf42061851262412f5feb.content". biodb.DEBUG[2024-07-06 16:03:25.793][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.794][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.794][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.798][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.799][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.800][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.802][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.804][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.805][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.809][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:25.812][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.813][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.814][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.818][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.819][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.821][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.825][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.828][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:25.832][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.832][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.833][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.838][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.840][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.844][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:25.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:25.851][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:25.853][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.853][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.854][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.858][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.859][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.860][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.862][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.869][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.870][private$selectFields] biodb.TRACE[2024-07-06 16:03:25.870][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:25.871][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:25.872][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.873][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.874][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.880][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.881][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.882][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.883][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.884][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.885][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.886][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.887][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.888][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.889][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.890][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.891][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.892][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:25.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.902][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.903][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-07-06 16:03:25.904][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.905][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.911][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.913][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.917][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.920][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.921][private$selectFields] biodb.TRACE[2024-07-06 16:03:25.922][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:25.923][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:25.924][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.924][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.925][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.926][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.927][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.928][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.929][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.930][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.931][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.931][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.932][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.933][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.934][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.935][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.936][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.937][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:25.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.941][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.948][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-07-06 16:03:25.949][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.950][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:25.955][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:25.955][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:25.956][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:25.957][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:25.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.965][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.966][private$selectFields] biodb.TRACE[2024-07-06 16:03:25.967][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:25.968][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:25.968][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.969][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.970][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.971][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.972][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.973][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.974][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.975][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.975][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.976][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.977][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:25.978][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.979][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.980][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.981][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.981][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:25.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.986][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.990][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:25.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:25.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:25.993][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [19804]. biodb.DEBUG[2024-07-06 16:03:25.994][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:25.995][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:25.997][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:25.998][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:25.999][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.003][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.004][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.005][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:26.008][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:26.010][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:03:26.012][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26d0872875c47c33e8205aa7124e0486". biodb.TRACE[2024-07-06 16:03:26.013][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:03:26.014][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26d0872875c47c33e8205aa7124e0486.content". biodb.DEBUG[2024-07-06 16:03:26.016][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.017][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.186][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.187][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.195][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.196][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.200][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.207][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.208][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.212][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.219][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.220][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.225][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.226][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.232][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.235][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.238][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.239][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.244][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.245][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.246][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.258][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.258][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.259][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.265][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.266][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.270][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.273][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.277][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.278][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.278][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.282][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.284][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.286][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.293][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.296][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.297][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.303][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.304][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.305][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.309][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.312][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.316][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.317][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.317][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.321][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.322][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.323][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.324][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.328][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.332][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.337][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:26.340][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:03:26.341][cch$loadFileContent] Trying to load 1 files from cache: [1]: "357534c211a0779cb44e196fcebae6c0". biodb.TRACE[2024-07-06 16:03:26.342][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:03:26.343][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/357534c211a0779cb44e196fcebae6c0.content". biodb.DEBUG[2024-07-06 16:03:26.346][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.347][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.352][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.354][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.360][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.364][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.368][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.369][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.376][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.382][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.386][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.389][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.390][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.397][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.398][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.398][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.401][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.404][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.412][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.413][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:26.414][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.423][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.432][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.433][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.434][private$selectFields] biodb.TRACE[2024-07-06 16:03:26.435][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:26.436][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:26.437][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.438][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.439][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.440][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.441][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.442][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.443][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.444][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.445][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.446][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.447][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.448][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.449][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.450][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.451][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.452][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:26.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.457][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.465][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-07-06 16:03:26.466][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.467][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.473][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.474][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.475][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.477][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.485][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.486][private$selectFields] biodb.TRACE[2024-07-06 16:03:26.487][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:26.488][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:26.493][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.494][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.495][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.495][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.496][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.497][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.498][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.499][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.500][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.501][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.501][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.502][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.503][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.504][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.505][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.506][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:26.507][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.510][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.517][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [71954]. biodb.DEBUG[2024-07-06 16:03:26.518][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.526][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.531][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.534][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.535][private$selectFields] biodb.TRACE[2024-07-06 16:03:26.536][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:26.537][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:26.538][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.539][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.540][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.540][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.541][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.542][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.543][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.544][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.545][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.546][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.547][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.547][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.548][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.549][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.550][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.551][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:26.552][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.559][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.561][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.562][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [197612]. biodb.DEBUG[2024-07-06 16:03:26.563][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:26.564][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:26.580][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.581][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.582][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.585][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.587][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:26.590][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.7*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:26.593][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:03:26.594][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2b6f29bb7a7663ff23fb5e7dcae5c27f". biodb.TRACE[2024-07-06 16:03:26.595][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:03:26.596][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2b6f29bb7a7663ff23fb5e7dcae5c27f.content". biodb.DEBUG[2024-07-06 16:03:26.598][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.599][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.600][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.603][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.605][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.607][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.610][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.617][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.618][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.623][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.624][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.626][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.630][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.636][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.637][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.644][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.655][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.656][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.663][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.665][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.671][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.672][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.674][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.675][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.677][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.681][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.682][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.682][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.688][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.695][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.696][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.697][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.702][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.715][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:26.716][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.723][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.732][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.733][private$selectFields] biodb.TRACE[2024-07-06 16:03:26.734][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:26.734][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:26.735][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.736][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.737][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.738][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.739][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.740][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.741][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.742][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.742][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.743][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.744][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.745][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.746][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.747][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.748][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.749][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:26.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.761][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-07-06 16:03:26.762][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.769][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.774][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.782][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.783][private$selectFields] biodb.TRACE[2024-07-06 16:03:26.784][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:26.785][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:26.786][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.786][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.787][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.788][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.789][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.790][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.791][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.792][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.793][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.793][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.794][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.795][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.796][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.797][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.798][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.799][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:26.799][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.806][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.807][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.810][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [28243]. biodb.DEBUG[2024-07-06 16:03:26.811][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.819][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.819][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.824][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.828][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.828][private$selectFields] biodb.TRACE[2024-07-06 16:03:26.829][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:26.830][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:26.831][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.832][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.833][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.834][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.834][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.835][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.836][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.837][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.838][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.839][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.840][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.840][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.841][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.842][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.843][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.844][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:26.845][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.848][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.855][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [78144]. biodb.DEBUG[2024-07-06 16:03:26.856][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:26.857][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:26.859][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.864][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.866][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:26.869][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.6*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:26.872][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:03:26.873][cch$loadFileContent] Trying to load 1 files from cache: [1]: "9a13652ab89a613a3b0e10d3b6cb10a0". biodb.TRACE[2024-07-06 16:03:26.874][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:03:26.875][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9a13652ab89a613a3b0e10d3b6cb10a0.content". biodb.DEBUG[2024-07-06 16:03:26.879][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.880][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.881][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.886][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.887][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.888][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.891][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.895][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.898][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.906][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.911][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.915][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.918][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.919][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.924][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.925][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.930][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:26.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:26.938][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:26.939][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.940][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.946][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.952][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.955][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.956][private$selectFields] biodb.TRACE[2024-07-06 16:03:26.957][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:26.958][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:26.959][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.959][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.960][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.961][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.962][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.963][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.964][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.965][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.966][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.966][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.967][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:26.968][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.969][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.970][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.971][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.972][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:26.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.980][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.984][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-07-06 16:03:26.985][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:26.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:26.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:26.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:26.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:26.992][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:26.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:26.994][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:26.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:26.997][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:26.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.001][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.002][private$selectFields] biodb.TRACE[2024-07-06 16:03:27.003][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:27.003][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:27.004][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.005][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.006][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.007][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.008][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.009][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.010][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.010][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.011][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.012][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.013][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.014][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.015][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.016][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.016][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.017][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:27.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.029][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-07-06 16:03:27.030][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.031][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.037][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.039][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.043][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.046][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.047][private$selectFields] biodb.TRACE[2024-07-06 16:03:27.048][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:27.049][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:27.049][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.050][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.051][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.052][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.053][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.054][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.055][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.056][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.057][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.057][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.058][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.059][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.060][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.061][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.062][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.063][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:27.068][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.075][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.079][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [19804]. biodb.DEBUG[2024-07-06 16:03:27.080][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:27.080][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:27.082][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.087][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.089][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:27.092][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.3*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:27.095][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:03:27.096][cch$loadFileContent] Trying to load 1 files from cache: [1]: "a985300ab8a01d49254fbf993ad91279". biodb.TRACE[2024-07-06 16:03:27.097][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:03:27.098][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a985300ab8a01d49254fbf993ad91279.content". biodb.DEBUG[2024-07-06 16:03:27.101][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.106][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.108][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.110][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.113][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.117][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.120][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.127][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.140][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.147][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.159][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.160][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.164][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.165][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.166][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.167][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.171][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.174][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.178][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.179][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.180][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.184][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.184][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.185][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.186][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.194][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.198][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.199][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.205][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.210][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.213][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.217][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.218][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.219][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.224][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.226][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.229][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.233][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.236][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.237][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.243][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.244][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.249][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.252][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.256][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.263][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.265][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.268][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.275][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.276][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.280][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.281][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.282][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.291][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.295][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.295][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.301][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.301][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.303][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.309][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.310][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.314][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.315][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.319][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.321][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.326][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.330][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.333][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.338][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.339][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.340][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.342][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.345][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.349][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.357][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.358][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.364][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.364][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.365][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.369][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.376][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.381][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.383][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.383][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.391][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.395][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.396][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.396][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.402][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.404][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.407][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.411][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.414][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.421][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.423][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.426][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.432][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.433][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.434][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.439][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.440][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.440][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.442][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.446][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.448][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.449][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.452][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.453][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.453][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.460][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.465][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.468][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.472][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.479][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.481][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.484][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.488][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.491][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.491][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.499][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.500][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.504][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.507][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.511][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.516][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.518][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.520][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.523][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.531][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.538][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.550][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.551][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.557][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.563][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.570][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.571][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.577][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.579][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.582][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.586][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.589][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.589][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.591][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.595][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.597][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.609][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.610][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.616][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.618][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.629][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.629][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.630][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.636][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.642][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:27.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.652][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:27.654][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.660][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.661][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.670][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.670][private$selectFields] biodb.TRACE[2024-07-06 16:03:27.671][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:27.672][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:27.673][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.674][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.675][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.676][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.676][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.677][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.678][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.679][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.680][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.681][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.682][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.682][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.683][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.684][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.685][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.686][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:27.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.693][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.694][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.698][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-07-06 16:03:27.699][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.699][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.700][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.706][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.707][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.714][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.715][private$selectFields] biodb.TRACE[2024-07-06 16:03:27.716][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:27.717][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:27.718][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.719][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.720][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.720][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.721][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.722][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.723][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.724][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.725][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.726][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.726][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.727][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.728][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.729][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.730][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.731][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:27.732][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.739][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.743][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [71954]. biodb.DEBUG[2024-07-06 16:03:27.744][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.751][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:27.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.760][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.761][private$selectFields] biodb.TRACE[2024-07-06 16:03:27.762][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:27.763][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:27.764][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.765][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.766][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.766][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.767][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.768][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.769][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.770][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.771][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.772][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.773][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:27.773][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.774][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.775][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.776][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.777][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:27.778][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.781][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:27.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.789][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [197612]. biodb.DEBUG[2024-07-06 16:03:27.790][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:27.791][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-07-06 16:03:27.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.812][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.820][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.827][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.838][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.841][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:27.845][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:27.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:27.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:27.850][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:27.851][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:27.852][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:27.856][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:27.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:27.857][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:27.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:27.861][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:27.864][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:27.864][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:27.866][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:03:28.273][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:03:28.939][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:28.943][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a035d13a630066423fab6713592c5e52.content" biodb.TRACE[2024-07-06 16:03:28.951][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a035d13a630066423fab6713592c5e52.request" biodb.DEBUG[2024-07-06 16:03:28.964][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:28.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:28.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:28.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:28.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:28.981][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:28.982][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:28.984][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:28.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:28.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:28.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:28.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:28.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:28.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:28.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:28.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:28.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:29.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:29.003][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:29.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:29.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:29.010][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:29.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:29.012][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:29.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:29.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:29.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:29.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:29.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:29.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:29.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:29.027][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:29.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:29.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:29.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:29.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:29.042][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:29.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:29.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:29.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:29.047][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:29.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:29.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:29.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:29.054][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:29.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:29.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:29.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:29.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:29.061][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:29.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:29.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:29.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:29.066][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:29.069][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:29.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:29.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:29.073][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:29.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:29.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:29.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:29.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:29.080][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:29.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:29.082][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:29.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:29.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:29.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:29.089][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:29.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:29.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:29.093][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:29.093][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:29.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:29.098][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:29.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:29.099][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:29.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:29.101][private$loadEntries] Creating entries from ids [1]: "9442". biodb.DEBUG[2024-07-06 16:03:29.102][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:29.104][cch$loadFileContent] Trying to load 1 files from cache: [1]: "9442". biodb.TRACE[2024-07-06 16:03:29.105][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:29.106][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:29.107][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:29.107][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:29.108][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:29.109][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:29.111][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:29.112][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:29.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:29.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:29.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:29.118][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:29.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:29.120][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=9442". biodb.DEBUG[2024-07-06 16:03:29.123][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:29.123][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:29.125][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=9442". biodb.TRACE[2024-07-06 16:03:29.521][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=9442). biodb.DEBUG[2024-07-06 16:03:29.951][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:29.956][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7d1576b26aed79f4c1d758a3f87c749b.content" biodb.TRACE[2024-07-06 16:03:29.962][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7d1576b26aed79f4c1d758a3f87c749b.request" biodb.TRACE[2024-07-06 16:03:29.967][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9442.xml" biodb.DEBUG[2024-07-06 16:03:29.970][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:29.973][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:29.975][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:29.979][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:29.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:29.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:29.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:29.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:29.995][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:29.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:30.001][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:30.002][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:30.004][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.006][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:30.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:30.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.014][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:30.015][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:30.016][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.018][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.019][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:30.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:30.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.024][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:30.025][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:30.026][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.028][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.029][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:30.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:30.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.033][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:30.035][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:30.036][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.036][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.038][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:30.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:30.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.042][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:30.043][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:30.044][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.044][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.046][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:30.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:30.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.049][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:30.050][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:30.051][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.052][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.053][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:30.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:30.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.056][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:30.057][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:30.058][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.059][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.060][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:30.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:30.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.064][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:30.065][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:30.066][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.066][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:30.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:30.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.071][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:30.072][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:30.073][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.074][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.075][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:30.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:30.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.078][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:30.079][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:30.080][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.081][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.082][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:30.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:30.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.086][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:30.087][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:30.088][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.088][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.090][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:30.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:30.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.093][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:30.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:30.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.097][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:30.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:30.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:30.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:30.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.104][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:30.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:30.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:30.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:30.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:30.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:30.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:30.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:30.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:30.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:30.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:30.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:30.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:30.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:30.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:30.129][self$createEntryFromContent] Accession numbers: 9442. biodb.TRACE[2024-07-06 16:03:30.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:30.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:30.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.133][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:30.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:30.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:30.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:30.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:30.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:30.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:30.140][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:30.141][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:30.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:30.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:30.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:30.148][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:30.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:30.149][private$loadEntries] Creating entries from ids [1]: "34764". biodb.DEBUG[2024-07-06 16:03:30.150][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:30.152][cch$loadFileContent] Trying to load 1 files from cache: [1]: "34764". biodb.TRACE[2024-07-06 16:03:30.153][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:30.154][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:30.155][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:30.156][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:30.157][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:30.157][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:30.160][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:30.161][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:30.161][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:30.166][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:30.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:30.167][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:30.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:30.169][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=34764". biodb.DEBUG[2024-07-06 16:03:30.172][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:30.172][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:30.174][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=34764". biodb.TRACE[2024-07-06 16:03:30.569][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=34764). biodb.DEBUG[2024-07-06 16:03:31.006][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:31.014][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a38508ac0dc37ed2da31f7bda33ae97f.content" biodb.TRACE[2024-07-06 16:03:31.023][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a38508ac0dc37ed2da31f7bda33ae97f.request" biodb.TRACE[2024-07-06 16:03:31.029][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/34764.xml" biodb.DEBUG[2024-07-06 16:03:31.032][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:31.035][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:31.038][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:31.042][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:31.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:31.078][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:31.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:31.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:31.086][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:31.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:31.090][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:31.091][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:31.092][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.093][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.094][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:31.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:31.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.098][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:31.099][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:31.100][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.101][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.102][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:31.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:31.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.106][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:31.107][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:31.108][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.109][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.111][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:31.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:31.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.114][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:31.116][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:31.116][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.117][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.119][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:31.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:31.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.123][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:31.124][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:31.125][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.125][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.127][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:31.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:31.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.131][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:31.132][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:31.133][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.133][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.135][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:31.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:31.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.139][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:31.140][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:31.141][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.141][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.143][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:31.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:31.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.147][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:31.148][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:31.148][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.149][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.151][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:31.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:31.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.155][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:31.156][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:31.157][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.157][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.159][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:31.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:31.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.163][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:31.164][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:31.165][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.166][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.167][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:31.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:31.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.171][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:31.172][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:31.173][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.174][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.175][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:31.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:31.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.178][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.179][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.183][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.186][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:31.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:31.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:31.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:31.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:31.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:31.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:31.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:31.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:31.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:31.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.209][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:31.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:31.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.213][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:31.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:31.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:31.217][self$createEntryFromContent] Accession numbers: 34764. biodb.TRACE[2024-07-06 16:03:31.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:31.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:31.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:31.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:31.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:31.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:31.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:31.230][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:31.232][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:31.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:31.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:31.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:31.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:31.239][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:31.240][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:31.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.249][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:31.250][private$selectFields] biodb.TRACE[2024-07-06 16:03:31.251][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:31.252][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:31.253][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:31.254][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.255][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.256][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.257][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.258][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.259][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.260][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.261][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.262][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:31.263][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:31.263][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.265][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.265][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.266][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.267][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:31.268][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.276][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.281][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [3014]. biodb.DEBUG[2024-07-06 16:03:31.282][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:31.283][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:31.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:31.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:31.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:31.290][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:31.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:31.292][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.296][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.299][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.300][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:31.301][private$selectFields] biodb.TRACE[2024-07-06 16:03:31.302][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:31.303][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:31.304][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:31.305][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.306][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.307][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.308][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.309][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.310][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.311][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.312][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.313][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:31.314][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:31.315][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.316][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.317][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.318][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.319][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:31.320][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.323][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.332][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-07-06 16:03:31.333][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:31.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:31.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:31.339][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:31.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:31.341][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:31.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:31.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.346][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.350][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:31.351][private$selectFields] biodb.TRACE[2024-07-06 16:03:31.352][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:31.353][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:31.354][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:31.355][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.356][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.357][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.358][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.359][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.360][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.361][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.362][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.363][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:31.364][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:31.365][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.366][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.366][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.367][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.368][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:31.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.377][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:31.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:31.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:31.381][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [34764]. biodb.DEBUG[2024-07-06 16:03:31.382][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:31.383][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:31.385][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:31.385][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:31.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:31.395][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:31.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:31.396][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:31.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:31.400][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:31.402][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:31.403][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:31.405][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:03:31.808][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:03:32.542][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:32.546][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/365d4ea5e0e90826806fec708da6c9ab.content" biodb.TRACE[2024-07-06 16:03:32.554][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/365d4ea5e0e90826806fec708da6c9ab.request" biodb.DEBUG[2024-07-06 16:03:32.565][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:32.566][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:32.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:32.574][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:32.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:32.577][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:32.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:32.579][private$loadEntries] Creating entries from ids [1]: "2535". biodb.DEBUG[2024-07-06 16:03:32.581][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:32.582][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2535". biodb.TRACE[2024-07-06 16:03:32.584][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:32.585][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:32.586][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:32.588][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:32.589][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:32.590][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:32.593][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:32.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:32.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:32.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:32.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:32.601][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:32.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:32.603][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2535". biodb.DEBUG[2024-07-06 16:03:32.605][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:32.606][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:32.607][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2535". biodb.TRACE[2024-07-06 16:03:32.997][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2535). biodb.DEBUG[2024-07-06 16:03:33.428][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:33.433][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e1d9514645c3005d4e4f643b2d18f099.content" biodb.TRACE[2024-07-06 16:03:33.439][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e1d9514645c3005d4e4f643b2d18f099.request" biodb.TRACE[2024-07-06 16:03:33.445][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2535.xml" biodb.DEBUG[2024-07-06 16:03:33.447][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:33.450][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:33.452][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:33.456][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:33.458][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:33.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:33.469][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:33.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:33.472][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:33.474][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:33.478][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:33.479][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:33.481][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.483][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.484][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:33.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:33.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.490][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:33.492][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:33.493][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.494][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.496][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:33.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:33.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.501][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:33.502][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:33.503][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.504][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.506][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:33.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:33.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.510][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:33.511][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:33.512][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.513][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:33.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:33.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.518][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:33.519][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:33.520][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.521][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.522][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:33.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:33.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.526][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:33.527][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:33.528][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.528][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.529][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:33.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:33.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.533][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:33.534][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:33.535][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.536][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.537][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:33.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:33.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.541][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:33.541][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:33.542][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.543][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:33.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:33.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.548][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:33.549][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:33.550][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.551][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.552][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:33.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:33.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.555][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:33.556][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:33.557][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.558][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.559][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:33.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:33.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.563][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:33.564][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:33.564][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.565][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.566][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:33.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:33.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.570][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:33.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:33.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:33.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:33.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.577][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:33.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:33.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:33.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:33.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:33.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:33.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:33.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:33.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:33.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:33.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.595][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:33.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:33.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:33.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:33.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:33.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:33.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:33.606][self$createEntryFromContent] Accession numbers: 2535. biodb.TRACE[2024-07-06 16:03:33.607][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:33.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:33.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:33.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:33.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:33.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:33.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:33.617][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:33.618][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:33.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:33.623][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:33.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:33.625][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:33.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:33.626][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:33.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:33.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.630][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:33.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:33.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:33.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:33.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:33.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:33.636][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:33.637][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:33.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:33.639][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:33.643][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:33.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:33.644][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:33.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:33.646][private$loadEntries] Creating entries from ids [1]: "5525". biodb.DEBUG[2024-07-06 16:03:33.647][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:33.648][cch$loadFileContent] Trying to load 1 files from cache: [1]: "5525". biodb.TRACE[2024-07-06 16:03:33.649][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:33.650][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:33.651][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:33.652][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:33.653][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:33.654][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:33.656][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:33.657][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:33.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:33.662][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:33.663][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:33.664][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:33.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:33.666][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=5525". biodb.DEBUG[2024-07-06 16:03:33.668][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:33.669][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:33.670][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=5525". biodb.TRACE[2024-07-06 16:03:34.093][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=5525). biodb.DEBUG[2024-07-06 16:03:34.763][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:34.768][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8c1563abc6b93d34a6b6b66375881583.content" biodb.TRACE[2024-07-06 16:03:34.774][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8c1563abc6b93d34a6b6b66375881583.request" biodb.TRACE[2024-07-06 16:03:34.779][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5525.xml" biodb.DEBUG[2024-07-06 16:03:34.782][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:34.785][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:34.787][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:34.791][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:34.793][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:34.795][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:34.804][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:34.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:34.808][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:34.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:34.830][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:34.832][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:34.833][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.834][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:34.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:34.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.840][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:34.841][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:34.842][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.843][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.845][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:34.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:34.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.849][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:34.850][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:34.851][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.852][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.853][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:34.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:34.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.857][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:34.858][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:34.858][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.859][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.860][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:34.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:34.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.863][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.864][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:34.865][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:34.866][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.867][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.868][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:34.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:34.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.871][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:34.872][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:34.873][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.874][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.875][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:34.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:34.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.878][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:34.879][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:34.880][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.881][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.882][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:34.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:34.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.886][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:34.886][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:34.887][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.888][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:34.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:34.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.893][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:34.894][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:34.894][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.895][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.896][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:34.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:34.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.900][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:34.901][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:34.902][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.903][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.904][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:34.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:34.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.907][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:34.908][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:34.909][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.910][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.911][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:34.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:34.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:34.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:34.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:34.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:34.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:34.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:34.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.924][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.925][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:34.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:34.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:34.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:34.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:34.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:34.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.935][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:34.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:34.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:34.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:34.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.942][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:34.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:34.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.945][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:34.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:34.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:34.949][self$createEntryFromContent] Accession numbers: 5525. biodb.TRACE[2024-07-06 16:03:34.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:34.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:34.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.954][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:34.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:34.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.957][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:34.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:34.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:34.961][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:34.962][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:34.962][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:34.967][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:34.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:34.968][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:34.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:34.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:34.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:34.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:34.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:34.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:34.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:34.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:34.981][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:34.982][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:34.983][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:34.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:34.988][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:34.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:34.989][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:34.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:34.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:34.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:34.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:34.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:34.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:34.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:34.998][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:34.999][private$selectFields] biodb.TRACE[2024-07-06 16:03:35.000][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:35.001][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:35.002][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:35.003][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.003][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.004][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.005][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.006][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.007][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.008][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.009][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.010][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:35.010][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:35.011][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.012][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.013][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.014][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.015][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:35.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.027][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [2535]. biodb.DEBUG[2024-07-06 16:03:35.028][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:35.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:35.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:35.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:35.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:35.035][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:35.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:35.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.044][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:35.045][private$selectFields] biodb.TRACE[2024-07-06 16:03:35.046][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:35.046][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:35.047][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:35.048][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.049][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.050][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.051][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.052][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.053][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.053][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.054][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.055][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:35.056][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:35.057][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.058][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.059][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.060][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.061][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:35.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.065][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.073][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-07-06 16:03:35.073][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:35.074][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:35.075][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:35.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:35.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:35.081][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:35.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:35.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.090][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:35.091][private$selectFields] biodb.TRACE[2024-07-06 16:03:35.092][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:35.092][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:35.093][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:35.094][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.095][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.096][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.097][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.098][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.099][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.100][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.101][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.101][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:35.102][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:35.103][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.104][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.105][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.106][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.107][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:35.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.119][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:35.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:35.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:35.123][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-07-06 16:03:35.124][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:35.125][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:35.127][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:35.127][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:35.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:35.132][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:35.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:35.134][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:35.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:35.137][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=409.9*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:35.140][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:35.140][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:35.142][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=409.9%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:03:35.534][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=409.9%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:03:35.944][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:35.948][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7b0416ab2d5cbf869f248000c039a8e8.content" biodb.TRACE[2024-07-06 16:03:35.956][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7b0416ab2d5cbf869f248000c039a8e8.request" biodb.DEBUG[2024-07-06 16:03:35.962][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:35.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:35.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:35.975][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:35.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:35.979][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:35.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:35.983][private$loadEntries] Creating entries from ids [1]: "31303". biodb.DEBUG[2024-07-06 16:03:35.985][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:35.988][cch$loadFileContent] Trying to load 1 files from cache: [1]: "31303". biodb.TRACE[2024-07-06 16:03:35.990][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:35.992][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:35.994][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:35.996][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:35.998][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:35.999][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:36.003][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:36.004][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:36.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:36.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:36.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:36.014][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:36.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:36.016][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=31303". biodb.DEBUG[2024-07-06 16:03:36.019][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:36.020][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:36.022][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=31303". biodb.TRACE[2024-07-06 16:03:36.424][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=31303). biodb.DEBUG[2024-07-06 16:03:36.852][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:36.856][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/99089a071b7e4bcfb0ef9a12b49b39b2.content" biodb.TRACE[2024-07-06 16:03:36.861][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/99089a071b7e4bcfb0ef9a12b49b39b2.request" biodb.TRACE[2024-07-06 16:03:36.865][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/31303.xml" biodb.DEBUG[2024-07-06 16:03:36.867][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:36.869][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:36.871][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:36.874][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:36.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:36.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:36.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:36.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:36.887][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:36.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:36.892][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:36.894][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:36.895][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.897][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.899][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:36.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:36.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.905][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:36.906][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:36.907][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.909][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.910][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:36.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:36.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.915][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:36.916][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:36.917][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.918][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.920][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:36.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:36.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.924][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:36.925][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:36.926][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.927][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.928][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:36.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:36.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.932][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:36.933][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:36.934][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.935][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.936][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:36.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:36.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.940][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:36.941][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:36.942][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.943][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.944][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:36.945][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:36.945][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.946][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.947][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:36.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:36.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.951][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:36.952][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:36.953][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.954][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:36.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:36.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.959][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:36.959][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:36.960][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.961][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.963][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:36.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:36.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.966][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:36.967][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:36.968][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.969][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.970][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:36.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:36.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.973][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:36.974][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:36.975][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.976][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.977][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:36.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:36.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:36.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:36.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.984][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:36.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:36.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.988][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:36.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:36.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:36.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:36.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:36.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:36.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:36.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:36.998][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:36.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:37.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:37.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:37.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:37.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:37.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:37.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:37.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:37.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:37.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:37.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:37.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:37.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:37.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:37.016][self$createEntryFromContent] Accession numbers: 31303. biodb.TRACE[2024-07-06 16:03:37.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:37.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:37.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:37.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:37.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:37.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:37.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:37.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:37.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:37.028][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:37.029][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:37.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:37.033][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:37.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:37.035][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:37.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:37.037][private$loadEntries] Creating entries from ids [1]: "37118". biodb.DEBUG[2024-07-06 16:03:37.038][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:37.039][cch$loadFileContent] Trying to load 1 files from cache: [1]: "37118". biodb.TRACE[2024-07-06 16:03:37.040][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:37.041][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:37.042][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:37.043][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:37.044][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:37.045][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:37.047][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:37.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:37.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:37.053][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:37.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:37.054][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:37.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:37.056][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=37118". biodb.DEBUG[2024-07-06 16:03:37.059][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:37.059][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:37.061][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=37118". biodb.TRACE[2024-07-06 16:03:37.458][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=37118). biodb.DEBUG[2024-07-06 16:03:37.889][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:37.893][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/37e09c6197385dffaf0a241198ec6309.content" biodb.TRACE[2024-07-06 16:03:37.900][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/37e09c6197385dffaf0a241198ec6309.request" biodb.TRACE[2024-07-06 16:03:37.905][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/37118.xml" biodb.DEBUG[2024-07-06 16:03:37.908][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:37.911][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:37.913][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:37.916][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:37.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:37.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:37.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:37.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:37.933][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:37.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:37.938][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:37.940][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:37.941][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.943][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:37.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:37.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:37.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:37.951][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:37.952][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:37.953][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.955][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:37.956][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:37.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:37.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:37.975][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:37.976][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:37.977][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.978][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:37.979][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:37.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:37.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:37.982][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:37.983][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:37.984][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.985][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:37.986][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:37.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:37.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:37.990][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:37.991][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:37.991][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.992][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:37.993][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:37.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:37.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:37.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:37.997][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:37.998][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:37.999][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.000][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.001][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:38.002][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:38.002][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.003][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.004][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:38.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:38.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.008][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:38.009][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:38.010][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.010][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.011][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:38.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:38.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.015][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:38.016][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:38.017][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.018][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.019][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:38.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:38.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.022][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:38.023][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:38.024][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.025][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.026][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:38.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:38.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.030][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:38.030][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:38.031][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.032][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.033][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:38.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:38.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.036][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:38.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:38.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.040][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:38.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:38.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:38.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:38.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.047][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:38.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:38.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.051][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:38.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:38.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.054][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:38.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:38.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:38.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:38.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.060][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:38.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:38.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.065][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:38.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:38.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:38.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:38.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:38.072][self$createEntryFromContent] Accession numbers: 37118. biodb.TRACE[2024-07-06 16:03:38.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:38.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:38.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:38.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:38.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.080][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:38.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:38.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:38.083][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:38.084][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:38.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:38.089][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:38.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:38.090][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:38.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:38.092][private$loadEntries] Creating entries from ids [1]: "39424". biodb.DEBUG[2024-07-06 16:03:38.093][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:38.095][cch$loadFileContent] Trying to load 1 files from cache: [1]: "39424". biodb.TRACE[2024-07-06 16:03:38.096][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:38.097][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:38.098][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:38.099][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:38.100][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:38.100][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:38.103][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:38.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:38.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:38.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:38.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:38.110][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:38.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:38.112][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=39424". biodb.DEBUG[2024-07-06 16:03:38.115][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:38.115][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:38.117][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=39424". biodb.TRACE[2024-07-06 16:03:38.513][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=39424). biodb.DEBUG[2024-07-06 16:03:38.907][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:38.909][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/da5bac251de02a0ce66c3d69c0d59bb8.content" biodb.TRACE[2024-07-06 16:03:38.912][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/da5bac251de02a0ce66c3d69c0d59bb8.request" biodb.TRACE[2024-07-06 16:03:38.914][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/39424.xml" biodb.DEBUG[2024-07-06 16:03:38.915][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:38.917][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:38.918][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:38.919][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:38.920][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:38.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:38.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:38.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:38.926][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:38.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:38.929][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:38.930][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:38.931][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.932][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:38.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:38.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.936][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:38.937][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:38.938][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.939][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.940][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:38.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:38.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.944][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:38.945][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:38.945][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.946][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.947][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:38.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:38.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.951][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:38.952][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:38.953][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.954][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.955][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:38.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:38.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.958][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:38.959][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:38.960][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.961][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.962][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:38.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:38.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.966][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:38.966][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:38.967][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.968][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.969][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:38.970][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:38.971][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.972][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.973][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:38.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:38.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.977][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:38.977][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:38.978][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.979][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:38.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:38.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.984][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:38.985][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:38.986][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.986][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:38.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:38.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.991][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:38.992][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:38.993][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.994][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.995][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:38.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:38.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:38.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:38.998][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:38.999][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:39.000][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.001][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.002][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:39.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:39.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:39.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:39.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:39.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:39.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:39.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:39.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:39.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:39.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:39.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:39.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:39.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:39.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:39.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:39.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:39.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:39.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:39.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:39.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:39.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:39.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:39.041][self$createEntryFromContent] Accession numbers: 39424. biodb.TRACE[2024-07-06 16:03:39.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:39.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:39.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.053][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:39.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:39.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.057][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:39.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:39.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:39.060][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:39.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:39.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:39.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:39.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:39.067][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:39.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:39.069][private$loadEntries] Creating entries from ids [1]: "81767". biodb.DEBUG[2024-07-06 16:03:39.070][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:39.071][cch$loadFileContent] Trying to load 1 files from cache: [1]: "81767". biodb.TRACE[2024-07-06 16:03:39.072][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:39.073][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:39.074][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:39.075][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:39.076][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:39.077][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:39.079][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:39.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:39.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:39.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:39.085][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:39.086][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:39.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:39.088][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=81767". biodb.DEBUG[2024-07-06 16:03:39.090][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:39.091][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:39.092][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=81767". biodb.TRACE[2024-07-06 16:03:39.500][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=81767). biodb.DEBUG[2024-07-06 16:03:39.895][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:39.897][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6d9dc9192959d977e17745ebfa06bb73.content" biodb.TRACE[2024-07-06 16:03:39.899][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6d9dc9192959d977e17745ebfa06bb73.request" biodb.TRACE[2024-07-06 16:03:39.902][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/81767.xml" biodb.DEBUG[2024-07-06 16:03:39.903][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:39.904][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:39.905][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:39.906][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:39.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:39.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:39.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:39.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:39.913][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:39.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:39.916][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:39.917][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:39.918][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.919][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:39.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:39.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.924][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:39.925][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:39.925][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.926][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.927][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:39.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:39.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.930][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.931][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:39.932][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:39.933][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.933][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.934][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:39.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:39.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.938][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:39.939][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:39.940][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.941][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.942][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:39.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:39.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.945][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:39.946][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:39.947][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.948][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.949][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:39.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:39.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.952][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:39.953][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:39.954][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.955][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.956][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:39.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:39.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.960][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:39.961][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:39.961][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.962][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.963][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:39.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:39.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.967][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:39.968][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:39.969][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.969][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.971][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:39.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:39.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.974][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:39.975][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:39.976][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.977][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.978][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:39.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:39.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.982][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:39.983][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:39.983][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.984][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.985][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:39.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:39.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.989][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:39.990][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:39.991][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.992][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.993][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:39.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:39.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:39.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:39.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:39.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:39.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:40.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:40.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:40.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:40.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.013][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:40.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:40.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:40.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:40.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:40.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:40.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:40.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:40.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:40.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:40.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:40.032][self$createEntryFromContent] Accession numbers: 81767. biodb.TRACE[2024-07-06 16:03:40.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:40.043][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.050][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:40.063][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:40.064][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.071][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.073][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.080][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.081][private$selectFields] biodb.TRACE[2024-07-06 16:03:40.082][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:40.083][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:40.084][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.085][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.086][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.086][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.087][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.088][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.089][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.090][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.091][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.092][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.092][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.093][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.094][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.095][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.096][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.097][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:40.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.101][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.104][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.105][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.109][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [31303]. biodb.DEBUG[2024-07-06 16:03:40.110][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.117][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.126][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.126][private$selectFields] biodb.TRACE[2024-07-06 16:03:40.127][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:40.128][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:40.129][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.130][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.138][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.139][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.140][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.141][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.141][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.142][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.143][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.144][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.145][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.146][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.147][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.147][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.148][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.149][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:40.150][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.161][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [81767]. biodb.DEBUG[2024-07-06 16:03:40.162][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.162][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.163][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.167][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.169][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.170][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.174][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.177][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.178][private$selectFields] biodb.TRACE[2024-07-06 16:03:40.179][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:40.180][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:40.181][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.182][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.183][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.183][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.184][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.185][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.186][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.187][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.188][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.188][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.189][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.190][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.191][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.192][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.193][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.194][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:40.195][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.198][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.201][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.205][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [131378]. biodb.DEBUG[2024-07-06 16:03:40.206][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:40.207][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:40.223][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.224][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.228][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.229][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:40.233][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:40.235][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:03:40.236][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2024-07-06 16:03:40.238][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:03:40.239][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2024-07-06 16:03:40.241][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:40.244][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:03:40.245][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2024-07-06 16:03:40.246][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:03:40.247][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2024-07-06 16:03:40.249][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.251][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.255][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.256][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.256][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.262][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.265][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:40.269][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.270][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.276][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.278][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:40.289][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.296][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.305][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:40.308][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:40.310][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.317][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.319][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.322][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.326][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.327][private$selectFields] biodb.TRACE[2024-07-06 16:03:40.328][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:40.328][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:40.329][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.330][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.331][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.332][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.333][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.334][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.335][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.336][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.336][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.337][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.338][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.339][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.340][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.341][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.342][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.342][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:40.343][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.354][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2024-07-06 16:03:40.355][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.356][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.357][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.363][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.372][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.372][private$selectFields] biodb.TRACE[2024-07-06 16:03:40.373][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:40.374][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:40.375][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.376][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.377][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.378][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.378][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.379][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.380][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.381][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.382][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.383][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.384][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.385][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.386][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.386][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.387][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.388][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:40.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.400][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-07-06 16:03:40.401][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.402][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.403][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.407][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.409][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.410][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.414][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.418][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.423][private$selectFields] biodb.TRACE[2024-07-06 16:03:40.424][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:40.425][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:40.426][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.426][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.427][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.428][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.429][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.430][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.431][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.432][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.433][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.433][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.434][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.435][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.436][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.437][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.438][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.439][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:40.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.447][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.449][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.450][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2024-07-06 16:03:40.451][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:40.452][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:40.454][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.455][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.455][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.459][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.461][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.462][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:40.464][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.29*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:40.467][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:03:40.468][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7269bbea581f1e243800f8ee4e0f4fdb". biodb.TRACE[2024-07-06 16:03:40.469][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:03:40.470][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7269bbea581f1e243800f8ee4e0f4fdb.content". biodb.DEBUG[2024-07-06 16:03:40.472][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.473][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.474][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.478][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.479][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.481][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.485][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.491][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:40.492][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.499][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:40.511][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.512][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.513][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.518][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:40.531][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:40.532][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.533][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.534][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.538][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.539][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.541][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.545][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.548][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.549][private$selectFields] biodb.TRACE[2024-07-06 16:03:40.550][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:40.551][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:40.552][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.552][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.553][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.554][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.555][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.556][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.557][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.558][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.559][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.559][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.560][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.561][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.562][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.563][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.564][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.565][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:40.566][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.569][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.573][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.577][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-07-06 16:03:40.578][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.578][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.583][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.584][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.585][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.589][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.594][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.595][private$selectFields] biodb.TRACE[2024-07-06 16:03:40.595][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:40.596][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:40.597][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.598][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.599][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.600][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.601][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.602][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.602][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.603][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.604][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.605][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.606][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.607][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.608][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.609][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.609][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.610][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:40.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.622][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [91601]. biodb.DEBUG[2024-07-06 16:03:40.623][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.624][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.629][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.630][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.632][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.635][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.639][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.639][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.640][private$selectFields] biodb.TRACE[2024-07-06 16:03:40.641][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:40.642][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:40.643][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.644][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.645][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.646][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.646][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.647][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.648][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.649][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.650][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.651][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.652][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.653][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.653][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.654][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.655][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.656][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:40.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.661][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.663][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.668][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [95147]. biodb.DEBUG[2024-07-06 16:03:40.669][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:40.670][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:40.671][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.672][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.673][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.679][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:40.682][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:40.685][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:03:40.686][cch$loadFileContent] Trying to load 1 files from cache: [1]: "acfa4b558978abf12409c2b56e678d03". biodb.TRACE[2024-07-06 16:03:40.687][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:03:40.688][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/acfa4b558978abf12409c2b56e678d03.content". biodb.DEBUG[2024-07-06 16:03:40.691][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.692][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.698][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.699][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.703][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.711][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:40.715][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.721][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.723][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.729][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:40.734][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.741][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.742][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:40.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:40.753][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:40.754][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.755][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.760][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.762][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.763][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.770][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.771][private$selectFields] biodb.TRACE[2024-07-06 16:03:40.772][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:40.773][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:40.774][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.775][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.775][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.776][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.777][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.778][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.779][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.780][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.781][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.781][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.782][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.783][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.784][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.785][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.786][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.787][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:40.787][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.791][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.794][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.798][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [636]. biodb.DEBUG[2024-07-06 16:03:40.799][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.800][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.805][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.806][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.811][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.815][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.816][private$selectFields] biodb.TRACE[2024-07-06 16:03:40.817][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:40.817][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:40.818][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.819][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.820][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.821][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.822][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.823][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.824][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.824][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.825][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.826][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.827][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.828][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.829][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.830][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.830][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.831][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:40.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.836][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.839][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.843][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [64199]. biodb.DEBUG[2024-07-06 16:03:40.844][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.851][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:40.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.857][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.860][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.861][private$selectFields] biodb.TRACE[2024-07-06 16:03:40.862][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:40.863][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:40.864][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.865][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.866][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.866][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.867][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.868][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.869][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.870][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.871][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.872][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.872][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:40.873][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.874][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.875][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.876][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.877][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:40.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.884][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.885][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:40.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:40.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:40.889][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [65648]. biodb.DEBUG[2024-07-06 16:03:40.890][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:40.890][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:40.907][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:40.907][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:40.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:40.912][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:40.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:40.913][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:40.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:40.917][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.3*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:40.920][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:40.921][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:40.922][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.3%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:03:41.311][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.3%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:03:41.697][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:41.699][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26eec570aadd234892b573eb0777bd78.content" biodb.TRACE[2024-07-06 16:03:41.702][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26eec570aadd234892b573eb0777bd78.request" biodb.DEBUG[2024-07-06 16:03:41.705][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:41.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:41.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:41.711][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:41.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:41.713][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:41.713][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:41.715][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:41.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:41.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:41.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:41.718][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:41.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:41.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:41.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:41.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:41.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:41.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:41.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:41.725][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:41.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:41.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:41.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:41.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:41.732][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:41.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:41.734][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:41.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:41.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:41.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:41.738][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:41.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:41.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:41.740][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:41.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:41.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:41.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:41.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:41.745][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:41.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:41.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:41.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:41.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:41.752][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:41.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:41.753][private$loadEntries] Creating entries from ids [1]: "17813". biodb.DEBUG[2024-07-06 16:03:41.754][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:41.756][cch$loadFileContent] Trying to load 1 files from cache: [1]: "17813". biodb.TRACE[2024-07-06 16:03:41.757][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:41.758][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:41.759][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:41.760][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:41.768][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:41.769][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:41.771][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:41.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:41.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:41.777][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:41.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:41.778][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:41.779][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:41.780][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17813". biodb.DEBUG[2024-07-06 16:03:41.783][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:41.783][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:41.785][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17813". biodb.TRACE[2024-07-06 16:03:42.189][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=17813). biodb.DEBUG[2024-07-06 16:03:42.583][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:42.586][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62f7e1534a05c51cc1431eff021df0bd.content" biodb.TRACE[2024-07-06 16:03:42.591][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62f7e1534a05c51cc1431eff021df0bd.request" biodb.TRACE[2024-07-06 16:03:42.595][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/17813.xml" biodb.DEBUG[2024-07-06 16:03:42.598][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:42.600][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:42.602][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:42.604][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:42.606][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:42.607][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:42.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:42.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:42.618][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:42.619][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:42.623][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:42.625][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:42.626][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.628][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.629][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:42.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:42.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.635][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:42.637][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:42.638][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.639][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.641][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:42.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:42.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.645][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.646][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:42.647][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:42.648][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.649][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.651][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:42.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:42.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.655][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:42.656][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:42.657][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.658][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.659][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:42.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:42.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.663][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:42.664][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:42.665][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.666][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:42.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:42.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.671][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:42.672][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:42.672][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.673][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.674][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:42.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:42.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.678][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:42.679][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:42.680][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.681][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.682][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:42.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:42.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.685][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:42.686][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:42.687][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.688][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:42.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:42.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.692][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:42.693][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:42.694][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.695][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:42.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:42.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.700][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:42.701][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:42.701][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.702][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.703][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:42.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:42.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.707][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:42.708][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:42.709][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.709][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.711][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:42.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:42.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:42.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:42.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:42.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:42.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.721][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:42.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:42.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:42.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:42.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.728][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:42.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:42.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:42.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:42.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:42.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:42.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:42.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:42.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:42.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:42.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:42.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:42.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:42.750][self$createEntryFromContent] Accession numbers: 17813. biodb.TRACE[2024-07-06 16:03:42.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:42.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:42.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.754][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:42.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:42.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:42.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:42.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:42.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:42.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:42.761][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:42.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:42.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:42.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:42.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:42.769][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:42.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:42.770][private$loadEntries] Creating entries from ids [1]: "30109". biodb.DEBUG[2024-07-06 16:03:42.771][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:42.773][cch$loadFileContent] Trying to load 1 files from cache: [1]: "30109". biodb.TRACE[2024-07-06 16:03:42.774][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:42.775][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:42.776][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:42.777][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:42.778][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:42.779][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:42.781][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:42.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:42.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:42.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:42.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:42.788][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:42.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:42.790][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=30109". biodb.DEBUG[2024-07-06 16:03:42.792][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:42.793][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:42.794][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=30109". biodb.TRACE[2024-07-06 16:03:43.220][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=30109). biodb.DEBUG[2024-07-06 16:03:43.662][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:43.666][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8ed09c4c418a18a426e08dad5ae6a3f9.content" biodb.TRACE[2024-07-06 16:03:43.673][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8ed09c4c418a18a426e08dad5ae6a3f9.request" biodb.TRACE[2024-07-06 16:03:43.678][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/30109.xml" biodb.DEBUG[2024-07-06 16:03:43.681][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:43.684][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:43.686][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:43.689][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:43.691][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:43.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:43.702][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:43.704][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:43.706][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:43.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:43.711][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:43.713][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:43.714][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.716][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:43.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:43.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.724][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:43.725][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:43.726][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.728][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.729][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:43.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:43.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.734][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:43.735][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:43.736][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.737][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.739][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:43.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:43.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.743][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:43.744][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:43.745][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.746][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.747][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:43.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:43.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.751][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:43.752][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:43.753][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.754][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.755][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:43.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:43.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.758][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.759][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:43.760][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:43.760][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.761][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.762][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:43.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:43.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.766][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:43.767][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:43.768][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.769][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.770][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:43.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:43.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.773][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:43.774][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:43.775][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.776][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:43.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:43.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.790][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:43.791][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:43.792][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.793][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:43.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:43.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.798][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:43.799][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:43.800][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.800][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.801][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:43.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:43.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.804][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.805][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:43.806][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:43.807][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.808][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.809][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:43.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:43.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.812][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:43.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:43.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:43.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:43.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:43.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:43.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:43.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:43.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:43.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:43.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:43.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:43.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.833][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:43.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:43.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.837][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:43.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:43.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:43.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:43.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.844][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:43.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:43.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:43.848][self$createEntryFromContent] Accession numbers: 30109. biodb.TRACE[2024-07-06 16:03:43.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:43.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:43.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:43.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:43.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:43.855][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:43.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:43.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:43.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:43.859][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:43.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:43.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:43.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:43.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:43.866][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:43.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:43.868][private$loadEntries] Creating entries from ids [1]: "33275". biodb.DEBUG[2024-07-06 16:03:43.869][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:43.870][cch$loadFileContent] Trying to load 1 files from cache: [1]: "33275". biodb.TRACE[2024-07-06 16:03:43.871][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:43.872][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:43.873][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:43.874][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:43.875][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:43.876][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:43.878][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:43.879][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:43.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:43.884][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:43.885][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:43.886][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:43.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:43.887][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=33275". biodb.DEBUG[2024-07-06 16:03:43.890][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:43.891][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:43.892][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=33275". biodb.TRACE[2024-07-06 16:03:44.283][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=33275). biodb.DEBUG[2024-07-06 16:03:44.723][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:44.727][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e7b5440dd739854267ce8eafb6ea36b1.content" biodb.TRACE[2024-07-06 16:03:44.734][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e7b5440dd739854267ce8eafb6ea36b1.request" biodb.TRACE[2024-07-06 16:03:44.739][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/33275.xml" biodb.DEBUG[2024-07-06 16:03:44.742][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:44.745][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:44.747][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:44.750][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:44.752][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:44.754][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:44.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:44.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:44.767][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:44.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:44.773][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:44.774][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:44.776][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.778][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:44.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:44.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.786][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:44.787][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:44.788][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.790][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.791][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:44.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:44.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.796][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:44.797][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:44.799][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.800][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.801][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:44.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:44.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.804][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.805][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:44.807][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:44.808][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.809][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.810][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:44.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:44.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.814][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:44.815][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:44.816][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.816][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.818][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:44.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:44.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.820][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.821][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:44.822][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:44.823][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.824][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.825][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:44.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:44.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.829][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:44.830][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:44.830][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.831][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.832][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:44.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:44.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.836][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:44.837][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:44.838][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.839][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:44.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:44.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.843][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:44.844][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:44.845][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.846][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:44.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:44.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.851][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:44.852][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:44.853][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.853][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.854][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:44.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:44.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.858][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:44.859][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:44.860][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.861][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.862][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:44.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:44.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.865][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:44.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:44.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.869][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:44.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:44.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.873][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:44.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:44.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.876][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:44.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:44.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:44.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:44.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.883][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:44.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:44.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:44.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:44.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:44.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:44.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.893][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:44.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:44.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.897][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:44.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:44.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:44.901][self$createEntryFromContent] Accession numbers: 33275. biodb.TRACE[2024-07-06 16:03:44.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:44.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:44.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:44.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:44.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.908][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:44.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:44.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:44.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:44.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:44.913][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:44.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:44.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:44.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:44.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:44.920][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:44.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:44.922][private$loadEntries] Creating entries from ids [1]: "33277". biodb.DEBUG[2024-07-06 16:03:44.922][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:44.924][cch$loadFileContent] Trying to load 1 files from cache: [1]: "33277". biodb.TRACE[2024-07-06 16:03:44.925][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:44.926][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:44.927][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:44.928][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:44.929][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:44.930][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:44.932][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:44.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:44.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:44.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:44.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:44.947][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:44.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:44.948][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=33277". biodb.DEBUG[2024-07-06 16:03:44.951][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:44.952][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:44.953][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=33277". biodb.TRACE[2024-07-06 16:03:45.584][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=33277). biodb.DEBUG[2024-07-06 16:03:46.281][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:46.286][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9e077bb25f478950bf1d29f1e643c2aa.content" biodb.TRACE[2024-07-06 16:03:46.292][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9e077bb25f478950bf1d29f1e643c2aa.request" biodb.TRACE[2024-07-06 16:03:46.298][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/33277.xml" biodb.DEBUG[2024-07-06 16:03:46.301][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:46.303][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:46.306][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:46.309][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:46.311][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:46.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:46.322][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:46.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:46.325][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:46.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:46.331][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:46.332][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:46.334][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.335][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:46.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:46.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.343][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:46.345][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:46.346][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.347][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.349][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:46.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:46.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.352][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.354][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:46.355][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:46.356][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.357][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.358][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:46.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:46.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.363][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:46.364][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:46.365][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.366][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.367][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:46.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:46.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.371][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:46.372][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:46.373][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.373][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.375][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:46.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:46.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.378][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:46.379][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:46.380][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.381][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.382][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:46.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:46.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.385][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:46.386][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:46.387][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.388][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.389][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:46.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:46.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.393][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:46.394][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:46.394][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.395][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:46.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:46.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.400][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:46.401][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:46.402][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.402][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.404][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:46.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:46.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.407][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:46.408][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:46.409][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.410][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.411][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:46.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:46.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.414][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:46.415][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:46.416][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.417][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.418][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:46.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:46.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.421][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:46.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:46.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:46.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:46.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:46.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:46.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:46.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:46.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.436][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:46.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:46.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.440][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:46.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:46.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.443][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:46.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:46.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.447][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:46.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:46.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.449][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.450][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:46.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:46.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:46.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:46.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:46.457][self$createEntryFromContent] Accession numbers: 33277. biodb.TRACE[2024-07-06 16:03:46.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:46.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:46.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.462][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:46.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:46.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:46.465][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:46.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:46.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:46.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:46.469][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:46.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:46.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:46.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:46.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:46.476][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:46.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:46.478][private$loadEntries] Creating entries from ids [1]: "52421". biodb.DEBUG[2024-07-06 16:03:46.479][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:46.480][cch$loadFileContent] Trying to load 1 files from cache: [1]: "52421". biodb.TRACE[2024-07-06 16:03:46.482][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:46.482][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:46.483][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:46.484][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:46.485][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:46.486][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:46.489][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:46.489][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:46.490][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:46.494][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:46.495][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:46.496][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:46.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:46.498][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=52421". biodb.DEBUG[2024-07-06 16:03:46.500][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:46.501][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:46.502][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=52421". biodb.TRACE[2024-07-06 16:03:46.923][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=52421). biodb.DEBUG[2024-07-06 16:03:47.358][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:47.362][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66d999f05cd47f00d9f023cd227b9481.content" biodb.TRACE[2024-07-06 16:03:47.369][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66d999f05cd47f00d9f023cd227b9481.request" biodb.TRACE[2024-07-06 16:03:47.374][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52421.xml" biodb.DEBUG[2024-07-06 16:03:47.377][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:47.379][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:47.382][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:47.385][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:47.387][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:47.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:47.398][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:47.400][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:47.401][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:47.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:47.407][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:47.409][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:47.410][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.412][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:47.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:47.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.418][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.419][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:47.421][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:47.422][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.423][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.425][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:47.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:47.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.430][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:47.431][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:47.432][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.433][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.435][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:47.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:47.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.439][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:47.440][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:47.441][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.442][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.443][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:47.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:47.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.447][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:47.448][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:47.449][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.450][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.451][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:47.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:47.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.455][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:47.456][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:47.456][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.457][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.458][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:47.459][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:47.460][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.461][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.462][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:47.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:47.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.466][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:47.467][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:47.467][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.468][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.469][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:47.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:47.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.473][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:47.474][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:47.475][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.476][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:47.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:47.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.480][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:47.481][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:47.486][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.493][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.494][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:47.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:47.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.498][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:47.499][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:47.499][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.500][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.501][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:47.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:47.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.511][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:47.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:47.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.515][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:47.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:47.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:47.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:47.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.526][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:47.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:47.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.528][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.529][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:47.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:47.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:47.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:47.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:47.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:47.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:47.540][self$createEntryFromContent] Accession numbers: 52421. biodb.TRACE[2024-07-06 16:03:47.541][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:47.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:47.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.544][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:47.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:47.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.548][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:47.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:47.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.550][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:47.551][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:47.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:47.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:47.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:47.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:47.558][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:47.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:47.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:47.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:47.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:47.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:47.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:47.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:47.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:47.571][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:03:47.572][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:47.573][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:47.574][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:47.577][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:47.578][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:47.579][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:47.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:47.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.588][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:47.588][private$selectFields] biodb.TRACE[2024-07-06 16:03:47.589][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:47.590][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:47.591][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:47.592][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.593][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.593][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.594][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.595][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.596][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.597][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.598][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.599][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:47.599][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:47.600][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.601][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.602][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.603][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.604][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:47.605][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.611][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.614][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.616][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2024-07-06 16:03:47.617][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:47.617][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:47.618][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:47.622][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:47.623][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:47.624][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:47.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:47.626][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.628][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.632][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.633][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:47.633][private$selectFields] biodb.TRACE[2024-07-06 16:03:47.634][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:47.635][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:47.636][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:47.637][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.638][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.639][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.639][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.640][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.641][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.642][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.643][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.644][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:47.645][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:47.645][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.646][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.647][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.648][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.649][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:47.650][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.653][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.656][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.657][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.661][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-07-06 16:03:47.662][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:47.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:47.663][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:47.667][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:47.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:47.669][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:47.670][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:47.671][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.674][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.678][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:47.679][private$selectFields] biodb.TRACE[2024-07-06 16:03:47.679][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:03:47.680][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:03:47.681][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:47.682][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.683][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.684][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.685][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.686][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.686][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.687][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.688][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.689][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:47.690][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:03:47.691][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.692][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.693][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.693][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.694][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:03:47.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.702][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:47.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:47.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:47.706][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2024-07-06 16:03:47.707][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:03:47.708][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:03:47.709][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:47.710][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:47.711][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:47.715][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:47.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:47.717][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:47.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:47.720][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.2*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:03:47.723][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:47.723][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:47.725][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.2%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". biodb.TRACE[2024-07-06 16:03:48.130][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.2%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL). biodb.DEBUG[2024-07-06 16:03:48.890][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:48.895][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/20c224089a82bbffabd2e7dbc67cfae3.content" biodb.TRACE[2024-07-06 16:03:48.903][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/20c224089a82bbffabd2e7dbc67cfae3.request" biodb.DEBUG[2024-07-06 16:03:48.917][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:48.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:48.920][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:48.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:48.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:48.933][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:48.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:48.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:48.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:48.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:48.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:48.943][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:48.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:48.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:48.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:48.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:48.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:48.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:48.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:48.955][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:48.956][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:48.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:48.962][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:48.963][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:48.964][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:48.965][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:48.966][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:48.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:48.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:48.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:48.979][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:48.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:48.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:48.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:48.982][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:48.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:48.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:48.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:48.986][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:48.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:48.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:48.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:48.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:48.993][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:48.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:48.995][private$loadEntries] Creating entries from ids [1]: "65567". biodb.DEBUG[2024-07-06 16:03:48.996][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:48.997][cch$loadFileContent] Trying to load 1 files from cache: [1]: "65567". biodb.TRACE[2024-07-06 16:03:48.998][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:48.999][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:49.000][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:49.001][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:49.002][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:49.003][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:49.005][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:49.006][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:49.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:49.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:49.011][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:49.012][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:49.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:49.014][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65567". biodb.DEBUG[2024-07-06 16:03:49.016][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:49.017][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:49.019][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65567". biodb.TRACE[2024-07-06 16:03:49.421][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65567). biodb.DEBUG[2024-07-06 16:03:49.860][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:49.863][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7f0d7a30f02eb1e897d8c17a3958aa76.content" biodb.TRACE[2024-07-06 16:03:49.869][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7f0d7a30f02eb1e897d8c17a3958aa76.request" biodb.TRACE[2024-07-06 16:03:49.873][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65567.xml" biodb.DEBUG[2024-07-06 16:03:49.875][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:49.877][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:49.879][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:49.882][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:49.883][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:49.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:49.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:49.894][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:49.895][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:49.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:49.900][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:49.902][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:49.903][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.905][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.907][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:49.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:49.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.913][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:49.914][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:49.915][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.917][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.918][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:49.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:49.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.923][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:49.924][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:49.926][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.927][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.928][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:49.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:49.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.932][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:49.933][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:49.934][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.935][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.936][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:49.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:49.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.940][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:49.941][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:49.942][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.943][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.944][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:49.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:49.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.948][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:49.949][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:49.950][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.950][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.952][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:49.952][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:49.953][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.954][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.955][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:49.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:49.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.959][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:49.960][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:49.961][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.961][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:49.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:49.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.966][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:49.967][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:49.968][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.969][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:49.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:49.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.974][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:49.974][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:49.975][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.976][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.977][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:49.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:49.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.981][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:49.982][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:49.983][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.983][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.985][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:49.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:49.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.988][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:49.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:49.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.992][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:49.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:49.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:49.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:49.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:49.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:49.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:50.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:50.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:50.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:50.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:50.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:50.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:50.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:50.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:50.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:50.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:50.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:50.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:50.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:50.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:50.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:50.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:50.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:50.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:50.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:50.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:50.023][self$createEntryFromContent] Accession numbers: 65567. biodb.TRACE[2024-07-06 16:03:50.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:50.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:50.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:50.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:50.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:50.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:50.032][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:50.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:50.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:50.035][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:50.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:50.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:50.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:50.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:50.042][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:50.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:50.044][private$loadEntries] Creating entries from ids [1]: "65576". biodb.DEBUG[2024-07-06 16:03:50.045][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:50.046][cch$loadFileContent] Trying to load 1 files from cache: [1]: "65576". biodb.TRACE[2024-07-06 16:03:50.048][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:50.049][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:50.050][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:50.050][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:50.051][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:50.052][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:50.055][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:50.055][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:50.056][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:50.060][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:50.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:50.062][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:50.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:50.063][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65576". biodb.DEBUG[2024-07-06 16:03:50.066][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:50.067][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:50.068][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65576". biodb.TRACE[2024-07-06 16:03:50.463][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=65576). biodb.DEBUG[2024-07-06 16:03:50.903][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:50.907][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/df387492c1d7c1e81f35830307d5d903.content" biodb.TRACE[2024-07-06 16:03:50.914][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/df387492c1d7c1e81f35830307d5d903.request" biodb.TRACE[2024-07-06 16:03:50.919][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65576.xml" biodb.DEBUG[2024-07-06 16:03:50.922][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:50.924][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:50.927][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:50.930][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:50.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:50.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:50.943][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:50.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:50.947][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:50.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:50.952][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:50.954][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:50.956][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.957][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:50.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:50.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:50.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:50.965][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:50.967][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:50.968][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.969][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:50.971][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:50.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:50.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:50.976][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:50.977][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:50.978][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.979][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:50.981][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:50.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:50.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.984][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:50.985][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:50.986][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:50.987][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.988][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:50.989][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:50.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:50.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:50.993][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:50.994][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:50.995][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:50.996][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.011][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:51.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:51.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.015][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:51.016][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:51.017][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.018][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.019][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:51.020][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:51.021][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.021][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.023][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:51.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:51.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.026][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:51.027][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:51.028][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.029][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:51.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:51.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.033][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:51.034][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:51.035][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.036][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.037][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:51.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:51.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.041][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:51.042][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:51.042][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.043][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.044][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:51.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:51.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.048][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:51.049][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:51.050][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.050][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.052][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:51.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:51.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.055][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:51.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:51.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:51.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:51.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:51.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:51.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:51.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:51.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:51.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:51.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:51.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:51.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.076][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:51.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:51.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:51.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:51.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:51.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:51.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.086][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:51.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:51.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:51.090][self$createEntryFromContent] Accession numbers: 65576. biodb.TRACE[2024-07-06 16:03:51.091][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:51.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:51.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.094][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:51.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:51.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.097][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:51.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:51.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:51.101][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:51.102][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:51.103][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:51.107][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:51.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:51.108][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:51.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:51.110][private$loadEntries] Creating entries from ids [1]: "66352". biodb.DEBUG[2024-07-06 16:03:51.111][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:51.113][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66352". biodb.TRACE[2024-07-06 16:03:51.114][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:51.115][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:51.116][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:51.117][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:51.117][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:51.118][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:51.121][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:51.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:51.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:51.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:51.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:51.128][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:51.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:51.130][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66352". biodb.DEBUG[2024-07-06 16:03:51.132][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:51.133][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:51.134][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66352". biodb.TRACE[2024-07-06 16:03:51.527][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66352). biodb.DEBUG[2024-07-06 16:03:51.914][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:51.916][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/45b0333aa11c1e7eb4af7d2d82f453d6.content" biodb.TRACE[2024-07-06 16:03:51.919][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/45b0333aa11c1e7eb4af7d2d82f453d6.request" biodb.TRACE[2024-07-06 16:03:51.921][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66352.xml" biodb.DEBUG[2024-07-06 16:03:51.922][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:51.923][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:51.924][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:51.926][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:51.927][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:51.927][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:51.931][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:51.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:51.933][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:51.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:51.936][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:51.937][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:51.938][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.938][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.939][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:51.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:51.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.943][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:51.944][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:51.945][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.946][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.947][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:51.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:51.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.950][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:51.951][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:51.952][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.953][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.954][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:51.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:51.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.958][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:51.959][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:51.959][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.960][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.961][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:51.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:51.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.965][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:51.966][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:51.967][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.968][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.969][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:51.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:51.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.972][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:51.973][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:51.974][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.975][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.976][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:51.977][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:51.978][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.979][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.980][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:51.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:51.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.983][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:51.984][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:51.985][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.986][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:51.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:51.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.991][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:51.991][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:51.992][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.993][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:51.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:51.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:51.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:51.998][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:51.999][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:52.000][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.001][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.002][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:52.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:52.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.005][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:52.006][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:52.007][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.008][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.009][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:52.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:52.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:52.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:52.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:52.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:52.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:52.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:52.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:52.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:52.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:52.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:52.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:52.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:52.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:52.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:52.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.036][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:52.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:52.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:52.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:52.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:52.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:52.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:52.048][self$createEntryFromContent] Accession numbers: 66352. biodb.TRACE[2024-07-06 16:03:52.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:52.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:52.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.052][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:52.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:52.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.056][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:52.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:52.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:52.059][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:52.060][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:52.061][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:52.065][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:52.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:52.067][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:52.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:52.068][private$loadEntries] Creating entries from ids [1]: "67567". biodb.DEBUG[2024-07-06 16:03:52.069][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:52.078][cch$loadFileContent] Trying to load 1 files from cache: [1]: "67567". biodb.TRACE[2024-07-06 16:03:52.080][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:52.081][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:52.082][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:52.083][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:52.083][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:52.084][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:52.087][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:52.087][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:52.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:52.092][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:52.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:52.094][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:52.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:52.095][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67567". biodb.DEBUG[2024-07-06 16:03:52.098][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:52.099][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:52.100][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67567". biodb.TRACE[2024-07-06 16:03:52.486][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67567). biodb.DEBUG[2024-07-06 16:03:52.932][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:52.934][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ef82f494f4fdd41c2bb93aa0869ad73e.content" biodb.TRACE[2024-07-06 16:03:52.937][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ef82f494f4fdd41c2bb93aa0869ad73e.request" biodb.TRACE[2024-07-06 16:03:52.939][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/67567.xml" biodb.DEBUG[2024-07-06 16:03:52.940][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:52.941][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:52.942][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:52.944][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:52.944][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:52.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:52.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:52.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:52.951][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:52.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:52.954][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:52.955][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:52.956][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.956][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:52.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:52.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.961][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:52.962][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:52.963][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.964][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.965][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:52.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:52.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.968][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:52.969][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:52.970][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.971][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.972][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:52.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:52.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.976][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:52.977][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:52.977][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.978][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.979][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:52.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:52.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.983][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:52.984][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:52.985][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.985][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.987][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:52.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:52.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.990][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:52.991][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:52.992][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.993][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.994][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:52.995][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:52.996][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:52.996][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:52.997][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:52.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:52.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.001][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:53.002][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:53.003][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.004][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:53.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:53.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.008][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:53.009][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:53.010][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.011][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.012][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:53.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:53.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.016][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:53.017][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:53.017][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.018][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.019][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:53.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:53.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.023][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:53.024][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:53.025][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.025][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.027][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:53.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:53.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.030][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:53.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:53.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:53.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:53.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.036][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:53.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:53.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.041][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:53.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:53.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.045][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:53.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:53.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:53.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:53.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:53.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:53.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:53.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:53.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:53.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:53.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:53.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:53.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:53.066][self$createEntryFromContent] Accession numbers: 67567. biodb.TRACE[2024-07-06 16:03:53.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:53.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:53.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:53.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:53.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:53.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:53.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:53.078][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:53.079][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:53.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:53.084][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:53.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:53.085][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:53.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:53.087][private$loadEntries] Creating entries from ids [1]: "67693". biodb.DEBUG[2024-07-06 16:03:53.088][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:53.089][cch$loadFileContent] Trying to load 1 files from cache: [1]: "67693". biodb.TRACE[2024-07-06 16:03:53.091][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:53.092][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:53.093][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:53.093][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:53.094][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:53.095][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:53.098][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:53.098][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:53.099][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:53.103][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:53.104][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:53.105][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:53.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:53.107][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67693". biodb.DEBUG[2024-07-06 16:03:53.109][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:53.110][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:53.111][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67693". biodb.TRACE[2024-07-06 16:03:53.505][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67693). biodb.DEBUG[2024-07-06 16:03:53.895][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:53.897][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/007181120197262f6a39eff57d7aa092.content" biodb.TRACE[2024-07-06 16:03:53.900][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/007181120197262f6a39eff57d7aa092.request" biodb.TRACE[2024-07-06 16:03:53.902][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/67693.xml" biodb.DEBUG[2024-07-06 16:03:53.903][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:53.904][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:53.906][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:53.907][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:53.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:53.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:53.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:53.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:53.914][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:53.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:53.917][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:53.918][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:53.919][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.920][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:53.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:53.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.924][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:53.925][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:53.926][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.927][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.928][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:53.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:53.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.932][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:53.933][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:53.934][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.934][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.935][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:53.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:53.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.939][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:53.940][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:53.941][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.942][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.943][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:53.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:53.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.945][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.946][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:53.947][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:53.948][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.949][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.950][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:53.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:53.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.954][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:53.955][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:53.956][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.957][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.958][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:53.959][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:53.959][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.960][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.961][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:53.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:53.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.965][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:53.966][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:53.967][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.968][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.969][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:53.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:53.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.972][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:53.978][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:53.985][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.986][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.987][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:53.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:53.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.991][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:53.992][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:53.993][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.993][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.995][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:53.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:53.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:53.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:53.998][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:53.999][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:54.000][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:54.001][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:54.002][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:54.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:54.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:54.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:54.005][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:54.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:54.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:54.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:54.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:54.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:54.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:54.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:54.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:54.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:54.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:54.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:54.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:54.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:54.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:54.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:54.019][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:54.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:54.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:54.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:54.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:54.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:54.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:54.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:54.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:54.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:54.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:54.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:54.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:54.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:54.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:54.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:54.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:54.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:54.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:54.036][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:54.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:54.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:54.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:54.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:54.041][self$createEntryFromContent] Accession numbers: 67693. biodb.TRACE[2024-07-06 16:03:54.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:54.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:54.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:54.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:54.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:54.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:54.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:54.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:54.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:54.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:54.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:54.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:54.052][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:54.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:54.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:54.058][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:54.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:54.059][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:54.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:54.061][private$loadEntries] Creating entries from ids [1]: "67700". biodb.DEBUG[2024-07-06 16:03:54.062][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:54.064][cch$loadFileContent] Trying to load 1 files from cache: [1]: "67700". biodb.TRACE[2024-07-06 16:03:54.065][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:54.066][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:54.067][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:54.068][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:54.068][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:54.069][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:54.072][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:54.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:54.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:54.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:54.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:54.079][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:54.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:54.081][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67700". biodb.DEBUG[2024-07-06 16:03:54.083][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:54.084][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:54.085][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67700". biodb.TRACE[2024-07-06 16:03:54.619][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67700). biodb.DEBUG[2024-07-06 16:03:55.012][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:55.014][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e41afa9432b74fa2b22a0c53e84c091a.content" biodb.TRACE[2024-07-06 16:03:55.017][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e41afa9432b74fa2b22a0c53e84c091a.request" biodb.TRACE[2024-07-06 16:03:55.019][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/67700.xml" biodb.DEBUG[2024-07-06 16:03:55.020][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:55.021][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:55.022][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:55.023][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:55.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:55.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:55.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:55.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:55.031][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:55.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:55.033][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:55.034][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:55.035][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.036][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.037][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:55.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:55.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.041][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:55.042][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:55.042][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.043][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.044][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:55.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:55.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.048][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:55.049][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:55.050][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.051][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.052][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:55.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:55.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.055][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:55.056][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:55.057][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.058][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.059][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:55.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:55.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.063][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:55.064][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:55.064][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.065][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.066][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:55.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:55.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.069][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.070][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:55.071][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:55.072][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.072][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.073][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:55.074][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:55.075][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.076][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.077][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:55.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:55.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.081][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:55.082][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:55.083][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.083][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.084][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:55.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:55.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.088][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:55.089][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:55.090][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.091][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.092][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:55.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:55.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.096][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:55.096][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:55.097][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.098][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.099][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:55.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:55.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.103][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:55.104][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:55.105][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.105][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.106][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:55.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:55.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.110][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:55.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:55.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.114][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:55.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:55.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:55.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:55.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.121][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:55.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:55.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:55.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:55.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.128][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:55.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:55.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:55.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:55.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:55.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:55.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.138][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:55.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:55.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:55.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:55.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:55.146][self$createEntryFromContent] Accession numbers: 67700. biodb.TRACE[2024-07-06 16:03:55.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:55.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:55.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:55.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:55.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.154][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:55.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:55.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:55.157][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:55.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:55.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:55.163][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:55.164][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:55.164][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:55.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:55.166][private$loadEntries] Creating entries from ids [1]: "67701". biodb.DEBUG[2024-07-06 16:03:55.167][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:55.169][cch$loadFileContent] Trying to load 1 files from cache: [1]: "67701". biodb.TRACE[2024-07-06 16:03:55.170][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:55.171][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:55.172][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:55.173][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:55.173][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:55.174][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:55.177][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:55.177][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:55.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:55.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:55.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:55.184][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:55.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:55.186][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67701". biodb.DEBUG[2024-07-06 16:03:55.188][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:55.189][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:55.190][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67701". biodb.TRACE[2024-07-06 16:03:55.582][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67701). biodb.DEBUG[2024-07-06 16:03:55.969][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:55.972][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ca9443fe11bfb8fe207e2797d18dbba3.content" biodb.TRACE[2024-07-06 16:03:55.974][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ca9443fe11bfb8fe207e2797d18dbba3.request" biodb.TRACE[2024-07-06 16:03:55.977][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/67701.xml" biodb.DEBUG[2024-07-06 16:03:55.978][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:55.979][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:55.980][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:55.981][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:55.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:55.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:55.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:55.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:55.988][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:55.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:55.991][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:55.992][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:55.993][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.994][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:55.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:55.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:55.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:55.999][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:55.999][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:56.000][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.001][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.002][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:56.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:56.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.006][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:56.007][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:56.008][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.008][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.010][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:56.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:56.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.013][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:56.014][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:56.015][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.016][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.017][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:56.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:56.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.020][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:56.021][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:56.022][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.023][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:56.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:56.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.028][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:56.029][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:56.029][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.030][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.031][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:56.032][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:56.033][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.034][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.035][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:56.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:56.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.038][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:56.039][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:56.040][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.041][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:56.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:56.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.046][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:56.047][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:56.047][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.048][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.049][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:56.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:56.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.053][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:56.054][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:56.055][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.056][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.057][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:56.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:56.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.060][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:56.061][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:56.062][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.063][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.064][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:56.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:56.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:56.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:56.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:56.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:56.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:56.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:56.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.078][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:56.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:56.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:56.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:56.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:56.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:56.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:56.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:56.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.092][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:56.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:56.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:56.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:56.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.099][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:56.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:56.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:56.103][self$createEntryFromContent] Accession numbers: 67701. biodb.TRACE[2024-07-06 16:03:56.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:56.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:56.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:56.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:56.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.111][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:56.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:56.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:56.114][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:56.115][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:56.116][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:56.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:56.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:56.122][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:56.123][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:56.123][private$loadEntries] Creating entries from ids [1]: "67705". biodb.DEBUG[2024-07-06 16:03:56.124][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:56.126][cch$loadFileContent] Trying to load 1 files from cache: [1]: "67705". biodb.TRACE[2024-07-06 16:03:56.127][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:56.128][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:56.129][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:56.130][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:56.131][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:56.132][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:56.134][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:56.135][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:56.135][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:56.139][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:56.140][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:56.141][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:56.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:56.143][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67705". biodb.DEBUG[2024-07-06 16:03:56.145][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:56.146][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:56.148][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67705". biodb.TRACE[2024-07-06 16:03:56.532][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67705). biodb.DEBUG[2024-07-06 16:03:56.924][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:56.926][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/19583a5be2f48ffe4ea86ed642cbc7df.content" biodb.TRACE[2024-07-06 16:03:56.929][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/19583a5be2f48ffe4ea86ed642cbc7df.request" biodb.TRACE[2024-07-06 16:03:56.931][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/67705.xml" biodb.DEBUG[2024-07-06 16:03:56.932][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:56.933][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:56.934][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:56.936][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:56.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:56.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:56.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:56.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:56.943][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:56.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:56.946][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:56.947][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:56.948][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.948][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.950][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:56.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:56.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.953][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:56.954][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:56.955][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.956][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.957][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:56.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:56.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.961][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:56.961][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:56.962][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.963][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.964][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:56.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:56.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.968][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:56.969][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:56.970][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.970][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:56.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:56.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.975][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:56.976][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:56.977][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.978][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.979][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:56.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:56.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.982][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:56.983][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:56.984][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.985][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.986][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:56.987][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:56.988][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.989][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.990][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:56.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:56.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.994][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:56.994][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:56.995][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:56.996][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:56.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:56.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:56.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.001][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:57.002][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:57.003][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.003][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.005][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:57.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:57.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.008][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:57.009][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:57.010][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.011][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.012][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:57.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:57.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.016][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:57.017][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:57.017][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.018][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.019][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:57.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:57.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:57.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:57.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.036][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:57.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:57.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:57.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:57.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.045][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:57.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:57.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.048][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:57.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:57.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:57.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:57.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:57.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:57.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:57.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:57.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:57.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:57.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:57.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:57.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:57.069][self$createEntryFromContent] Accession numbers: 67705. biodb.TRACE[2024-07-06 16:03:57.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:57.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:57.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:57.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:57.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.077][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:57.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:57.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:57.081][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:57.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:57.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:57.086][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:57.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:57.088][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:57.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:57.089][private$loadEntries] Creating entries from ids [1]: "75265". biodb.DEBUG[2024-07-06 16:03:57.090][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:57.092][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75265". biodb.TRACE[2024-07-06 16:03:57.093][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:57.094][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:57.095][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:57.096][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:57.097][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:57.097][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:57.100][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:57.100][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:57.101][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:57.105][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:57.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:57.107][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:57.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:57.108][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75265". biodb.DEBUG[2024-07-06 16:03:57.111][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:57.112][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:57.113][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75265". biodb.TRACE[2024-07-06 16:03:57.508][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75265). biodb.DEBUG[2024-07-06 16:03:57.898][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:57.900][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d89a3a12f8b9f5e8203e72f55b0016ed.content" biodb.TRACE[2024-07-06 16:03:57.902][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/d89a3a12f8b9f5e8203e72f55b0016ed.request" biodb.TRACE[2024-07-06 16:03:57.905][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75265.xml" biodb.DEBUG[2024-07-06 16:03:57.906][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:57.907][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:57.908][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:57.909][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:57.910][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:57.911][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:57.915][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:57.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:57.916][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:57.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:57.919][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:57.920][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:57.921][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.922][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.923][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:57.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:57.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.927][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:57.928][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:57.928][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.929][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.930][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:57.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:57.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.934][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:57.935][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:57.936][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.937][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.938][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:57.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:57.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.941][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:57.942][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:57.943][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.944][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.945][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:57.946][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:57.947][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.948][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.949][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:57.950][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:57.950][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.951][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.952][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:57.953][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:57.954][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.955][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.956][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:57.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:57.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.960][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:57.961][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:57.961][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.962][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.963][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:57.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:57.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.967][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:57.968][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:57.969][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.969][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.971][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:57.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:57.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.974][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:57.975][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:57.976][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.977][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.978][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:57.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:57.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.982][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:57.982][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:57.983][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.984][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.985][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:57.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:57.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.989][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:57.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:57.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:57.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:57.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:57.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:57.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:57.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:57.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.000][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:58.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:58.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.003][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:58.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:58.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.007][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:58.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:58.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.010][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:58.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:58.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.013][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.014][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:58.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:58.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:58.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:58.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:58.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:58.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:58.024][self$createEntryFromContent] Accession numbers: 75265. biodb.TRACE[2024-07-06 16:03:58.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:58.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:58.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:58.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:58.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:58.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:58.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:58.036][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:58.037][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:58.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:58.042][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:58.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:58.043][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:58.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:58.045][private$loadEntries] Creating entries from ids [1]: "77370". biodb.DEBUG[2024-07-06 16:03:58.046][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:58.048][cch$loadFileContent] Trying to load 1 files from cache: [1]: "77370". biodb.TRACE[2024-07-06 16:03:58.049][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:58.050][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:58.051][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:58.052][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:58.052][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:58.053][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:58.056][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:58.056][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:58.057][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:58.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:58.062][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:58.063][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:58.064][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:58.065][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77370". biodb.DEBUG[2024-07-06 16:03:58.067][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:58.068][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:58.069][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77370". biodb.TRACE[2024-07-06 16:03:58.452][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=77370). biodb.DEBUG[2024-07-06 16:03:58.843][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:58.845][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c00fcc12163fc12434466e6319d4b9a8.content" biodb.TRACE[2024-07-06 16:03:58.848][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c00fcc12163fc12434466e6319d4b9a8.request" biodb.TRACE[2024-07-06 16:03:58.850][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/77370.xml" biodb.DEBUG[2024-07-06 16:03:58.851][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:58.852][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:58.853][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:58.855][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:58.856][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:58.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:58.860][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:58.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:58.862][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:58.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:58.865][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:58.866][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:58.867][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.867][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:58.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:58.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.881][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.883][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:58.884][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:58.884][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.885][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.886][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:58.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:58.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.890][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:58.891][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:58.892][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.893][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.894][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:58.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:58.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.896][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.897][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:58.898][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:58.899][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.900][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.901][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:58.902][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:58.903][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.903][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.904][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:58.905][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:58.906][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.907][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.908][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:58.909][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:58.910][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.911][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.912][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:58.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:58.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.915][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:58.916][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:58.917][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.918][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.919][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:58.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:58.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.922][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:58.923][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:58.924][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.925][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.926][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:58.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:58.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.930][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:58.931][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:58.932][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.932][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.933][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:58.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:58.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.937][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:58.938][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:58.939][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.940][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.941][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:58.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:58.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:58.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:58.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.948][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:58.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:58.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:58.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:58.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:58.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:58.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:58.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:58.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.961][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:58.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:58.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:58.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:58.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:58.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:58.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:58.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:58.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.975][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:58.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:58.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:58.979][self$createEntryFromContent] Accession numbers: 77370. biodb.TRACE[2024-07-06 16:03:58.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:58.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:58.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:58.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:58.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:58.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:58.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:58.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:58.989][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:58.990][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:58.991][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:58.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:58.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:58.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:58.997][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:58.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:58.999][private$loadEntries] Creating entries from ids [1]: "79074". biodb.DEBUG[2024-07-06 16:03:59.000][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:59.002][cch$loadFileContent] Trying to load 1 files from cache: [1]: "79074". biodb.TRACE[2024-07-06 16:03:59.003][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:59.004][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:59.005][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:59.006][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:59.007][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:59.007][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:59.010][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:59.011][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:59.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:59.015][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:59.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:59.017][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:59.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:59.019][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79074". biodb.DEBUG[2024-07-06 16:03:59.021][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:59.022][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:59.024][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79074". biodb.TRACE[2024-07-06 16:03:59.410][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79074). biodb.DEBUG[2024-07-06 16:03:59.797][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:03:59.799][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9d103521a9057f87b1d7f6dac467847d.content" biodb.TRACE[2024-07-06 16:03:59.802][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/9d103521a9057f87b1d7f6dac467847d.request" biodb.TRACE[2024-07-06 16:03:59.804][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/79074.xml" biodb.DEBUG[2024-07-06 16:03:59.805][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:03:59.806][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:03:59.807][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:03:59.809][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:59.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:59.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:59.814][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:59.815][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:59.816][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:59.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:03:59.819][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:59.820][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:59.821][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.821][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:59.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:59.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.826][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:59.827][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:59.828][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.829][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.830][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:03:59.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:03:59.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.834][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:59.835][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:59.835][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.836][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.837][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:03:59.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:03:59.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.841][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:59.842][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:59.843][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.844][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.845][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:03:59.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:03:59.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.848][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:59.849][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:59.850][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.851][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.852][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:03:59.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:03:59.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.856][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:59.857][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:03:59.858][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.858][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.860][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:59.861][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:59.861][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.862][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.863][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:03:59.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:03:59.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.867][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:59.868][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:59.869][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.870][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:59.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:59.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.874][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:59.875][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:59.876][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.877][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.878][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:03:59.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:03:59.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.881][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.882][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:59.883][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:59.884][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.885][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.886][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:03:59.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:03:59.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.889][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:59.890][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:59.891][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.892][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.893][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:03:59.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:03:59.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.896][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.897][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:59.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:59.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.900][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:59.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:59.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.904][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:59.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:59.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.907][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:03:59.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:03:59.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.911][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:59.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:59.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.914][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.915][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:59.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:59.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:59.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:59.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.922][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:59.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:59.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:59.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:59.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:03:59.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:03:59.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:59.933][self$createEntryFromContent] Accession numbers: 79074. biodb.TRACE[2024-07-06 16:03:59.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:59.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:59.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.945][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.946][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:59.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:59.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:03:59.949][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:59.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:03:59.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:03:59.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:03:59.953][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:59.954][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:59.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:59.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:59.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:59.960][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:59.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:59.962][private$loadEntries] Creating entries from ids [1]: "79302". biodb.DEBUG[2024-07-06 16:03:59.963][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:03:59.964][cch$loadFileContent] Trying to load 1 files from cache: [1]: "79302". biodb.TRACE[2024-07-06 16:03:59.965][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:03:59.966][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:03:59.967][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:03:59.968][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:03:59.969][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:03:59.970][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:03:59.972][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:03:59.973][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:03:59.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:03:59.977][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:03:59.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:03:59.979][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:03:59.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:03:59.981][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79302". biodb.DEBUG[2024-07-06 16:03:59.983][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:03:59.984][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:03:59.985][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79302". biodb.TRACE[2024-07-06 16:04:00.382][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79302). biodb.DEBUG[2024-07-06 16:04:00.773][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:04:00.775][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/db109891c430ecee6c4d31019e936bb4.content" biodb.TRACE[2024-07-06 16:04:00.777][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/db109891c430ecee6c4d31019e936bb4.request" biodb.TRACE[2024-07-06 16:04:00.779][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/79302.xml" biodb.DEBUG[2024-07-06 16:04:00.781][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:04:00.782][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:04:00.783][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:04:00.784][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:00.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:00.786][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:00.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:00.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:00.791][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:00.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:00.794][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:00.795][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:00.796][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.797][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:00.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:00.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.800][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.801][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:00.802][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:00.803][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.804][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.805][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:00.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:00.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.808][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:00.809][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:00.810][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.811][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.812][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:00.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:00.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.816][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:00.816][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:00.817][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.818][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.819][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:00.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:00.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.823][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:00.824][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:00.824][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.825][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.826][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:00.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:00.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.830][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:00.831][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:00.832][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.832][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.833][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:00.834][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:00.835][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.836][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.837][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:00.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:00.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.841][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:00.842][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:00.843][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.843][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:00.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:00.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.848][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:00.849][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:00.850][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.851][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:00.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:00.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.855][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:00.856][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:00.857][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.858][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.859][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:00.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:00.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.863][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:00.864][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:00.865][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.865][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.866][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:00.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:00.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.870][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:00.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:00.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:00.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:00.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.876][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:00.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:00.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.881][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:00.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:00.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.884][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:00.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:00.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:00.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:00.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:00.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:00.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:00.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:00.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:00.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:00.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:00.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:00.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:00.905][self$createEntryFromContent] Accession numbers: 79302. biodb.TRACE[2024-07-06 16:04:00.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:00.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:00.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.909][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:00.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:00.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:00.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:00.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:00.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:00.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:00.917][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:00.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:00.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:00.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:00.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:00.924][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:00.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:00.926][private$loadEntries] Creating entries from ids [1]: "84164". biodb.DEBUG[2024-07-06 16:04:00.927][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:04:00.928][cch$loadFileContent] Trying to load 1 files from cache: [1]: "84164". biodb.TRACE[2024-07-06 16:04:00.929][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:04:00.930][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:04:00.931][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:04:00.932][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:04:00.933][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:04:00.934][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:04:00.936][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:00.937][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:00.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:00.942][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:00.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:00.944][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:00.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:00.945][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=84164". biodb.DEBUG[2024-07-06 16:04:00.948][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:04:00.949][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:04:00.950][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=84164". biodb.TRACE[2024-07-06 16:04:01.334][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=84164). biodb.DEBUG[2024-07-06 16:04:01.731][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:04:01.733][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5878d01d3db7a255abcfdf35c60dd985.content" biodb.TRACE[2024-07-06 16:04:01.736][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5878d01d3db7a255abcfdf35c60dd985.request" biodb.TRACE[2024-07-06 16:04:01.738][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/84164.xml" biodb.DEBUG[2024-07-06 16:04:01.739][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:04:01.740][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:04:01.741][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:04:01.743][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:01.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:01.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:01.748][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:01.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:01.750][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:01.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:01.753][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:01.753][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:01.754][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.755][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:01.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:01.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.760][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:01.761][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:01.762][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.763][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.764][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:01.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:01.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.767][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:01.768][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:01.769][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.770][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.771][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:01.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:01.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.775][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:01.775][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:01.776][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.777][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.778][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:01.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:01.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.782][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:01.783][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:01.784][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.784][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.790][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:01.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:01.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.800][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:01.801][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:01.802][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.803][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.804][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:01.805][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:01.805][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.806][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.807][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:01.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:01.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.811][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:01.812][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:01.813][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.813][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.815][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:01.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:01.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.818][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:01.819][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:01.820][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.821][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.822][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:01.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:01.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.825][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:01.826][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:01.827][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.828][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.829][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:01.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:01.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.833][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:01.833][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:01.834][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.835][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.836][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:01.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:01.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.840][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:01.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:01.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.843][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:01.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:01.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:01.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:01.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:01.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:01.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:01.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:01.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:01.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:01.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.860][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:01.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:01.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.863][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:01.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:01.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.867][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:01.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:01.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:01.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:01.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:01.875][self$createEntryFromContent] Accession numbers: 84164. biodb.TRACE[2024-07-06 16:04:01.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:01.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:01.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.878][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:01.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:01.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:01.883][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:01.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:01.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:01.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:01.886][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:01.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:01.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:01.892][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:01.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:01.893][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:01.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:01.895][private$loadEntries] Creating entries from ids [1]: "132314". biodb.DEBUG[2024-07-06 16:04:01.896][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:04:01.897][cch$loadFileContent] Trying to load 1 files from cache: [1]: "132314". biodb.TRACE[2024-07-06 16:04:01.898][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:04:01.899][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:04:01.900][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:04:01.901][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:04:01.902][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:04:01.903][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:04:01.905][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:01.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:01.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:01.911][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:01.912][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:01.912][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:01.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:01.914][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132314". biodb.DEBUG[2024-07-06 16:04:01.917][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:04:01.917][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:04:01.919][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132314". biodb.TRACE[2024-07-06 16:04:02.311][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132314). biodb.DEBUG[2024-07-06 16:04:02.714][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:04:02.716][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/faff8e4827734119a684907f214879a2.content" biodb.TRACE[2024-07-06 16:04:02.719][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/faff8e4827734119a684907f214879a2.request" biodb.TRACE[2024-07-06 16:04:02.721][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/132314.xml" biodb.DEBUG[2024-07-06 16:04:02.722][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:04:02.723][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:04:02.724][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:04:02.725][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:02.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:02.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:02.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:02.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:02.733][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:02.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:02.736][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:02.737][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:02.738][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.738][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:02.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:02.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.743][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:02.744][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:02.745][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.746][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.747][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:02.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:02.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.751][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:02.751][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:02.752][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.753][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.754][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:02.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:02.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.758][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:02.759][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:02.760][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.760][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.762][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:02.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:02.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.765][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:02.766][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:02.767][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.768][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.769][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:02.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:02.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.772][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:02.773][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:02.774][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.775][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.776][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:02.777][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:02.778][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.779][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.780][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:02.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:02.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.784][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:02.784][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:02.785][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.786][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.787][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:02.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:02.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.791][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:02.792][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:02.793][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.793][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.795][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:02.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:02.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.798][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:02.799][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:02.800][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.801][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.802][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:02.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:02.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.806][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:02.806][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:02.807][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.808][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.809][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:02.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:02.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.813][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:02.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:02.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.816][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:02.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:02.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.820][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:02.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:02.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:02.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:02.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.827][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:02.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:02.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.830][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:02.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:02.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:02.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:02.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:02.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:02.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.841][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:02.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:02.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.845][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:02.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:02.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:02.848][self$createEntryFromContent] Accession numbers: 132314. biodb.TRACE[2024-07-06 16:04:02.849][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:02.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:02.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.853][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:02.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:02.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:02.856][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:02.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:02.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:02.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:02.860][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:02.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:02.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:02.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:02.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:02.867][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:02.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:02.877][private$loadEntries] Creating entries from ids [1]: "132338". biodb.DEBUG[2024-07-06 16:04:02.878][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:04:02.879][cch$loadFileContent] Trying to load 1 files from cache: [1]: "132338". biodb.TRACE[2024-07-06 16:04:02.880][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:04:02.881][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:04:02.882][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:04:02.883][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:04:02.884][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:04:02.885][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:04:02.887][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:02.888][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:02.889][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:02.893][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:02.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:02.894][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:02.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:02.896][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132338". biodb.DEBUG[2024-07-06 16:04:02.898][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:04:02.899][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:04:02.900][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132338". biodb.TRACE[2024-07-06 16:04:03.287][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=132338). biodb.DEBUG[2024-07-06 16:04:03.681][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:04:03.683][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4ab2b9171a775a690a32a30e73cf2a1c.content" biodb.TRACE[2024-07-06 16:04:03.686][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4ab2b9171a775a690a32a30e73cf2a1c.request" biodb.TRACE[2024-07-06 16:04:03.688][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/132338.xml" biodb.DEBUG[2024-07-06 16:04:03.690][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:04:03.691][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:04:03.692][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:04:03.693][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:03.694][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:03.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:03.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:03.700][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:03.700][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:03.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:03.703][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:03.704][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:03.705][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.706][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.707][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:03.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:03.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.709][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.710][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:03.711][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:03.712][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.713][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.714][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:03.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:03.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.718][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:03.719][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:03.720][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.720][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.721][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:03.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:03.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.725][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:03.726][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:03.727][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.728][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.729][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:03.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:03.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.732][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:03.733][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:03.734][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.735][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.736][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:03.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:03.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.739][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.740][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:03.741][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:03.741][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.742][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.743][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:03.744][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:03.745][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.746][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.747][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:03.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:03.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.750][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:03.751][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:03.752][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.753][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.754][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:03.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:03.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.758][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:03.759][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:03.759][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.760][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:03.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:03.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.765][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:03.766][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:03.767][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.767][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.769][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:03.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:03.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.772][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:03.773][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:03.774][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.775][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.776][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:03.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:03.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.780][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:03.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:03.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:03.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:03.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:03.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:03.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.790][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:03.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:03.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.793][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:03.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:03.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:03.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:03.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.800][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:03.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:03.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:03.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:03.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:03.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:03.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:03.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:03.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:03.815][self$createEntryFromContent] Accession numbers: 132338. biodb.TRACE[2024-07-06 16:04:03.816][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:03.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:03.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:03.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:03.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:03.823][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:03.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:03.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:03.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:03.827][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:03.827][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:03.828][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:03.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:03.833][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:03.834][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:03.835][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:03.836][private$loadEntries] Creating entries from ids [1]: "139019". biodb.DEBUG[2024-07-06 16:04:03.836][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:04:03.838][cch$loadFileContent] Trying to load 1 files from cache: [1]: "139019". biodb.TRACE[2024-07-06 16:04:03.839][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:04:03.840][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:04:03.841][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:04:03.842][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:04:03.843][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:04:03.844][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:04:03.846][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:03.847][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:03.848][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:03.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:03.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:03.853][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:03.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:03.855][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=139019". biodb.DEBUG[2024-07-06 16:04:03.857][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:04:03.858][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:04:03.859][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=139019". biodb.TRACE[2024-07-06 16:04:04.244][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=139019). biodb.DEBUG[2024-07-06 16:04:04.633][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:04:04.635][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c6e6f1783364d5307c1e22caca9f3324.content" biodb.TRACE[2024-07-06 16:04:04.638][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c6e6f1783364d5307c1e22caca9f3324.request" biodb.TRACE[2024-07-06 16:04:04.640][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/139019.xml" biodb.DEBUG[2024-07-06 16:04:04.642][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:04:04.643][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:04:04.644][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:04:04.645][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:04.646][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:04.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:04.651][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:04.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:04.652][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:04.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:04.655][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:04.656][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:04.657][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.658][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.659][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:04.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:04.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.663][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:04.664][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:04.664][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.665][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.666][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:04.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:04.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.670][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:04.671][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:04.672][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.673][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.674][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:04.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:04.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.677][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:04.678][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:04.679][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.680][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.681][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:04.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:04.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.684][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:04.685][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:04.686][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.687][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.688][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:04.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:04.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.692][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:04.693][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:04.693][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.694][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.695][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:04.696][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:04.697][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.698][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.699][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:04.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:04.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.703][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:04.704][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:04.704][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.705][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:04.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:04.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.721][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:04.722][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:04.723][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.723][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.725][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:04.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:04.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.728][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:04.729][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:04.730][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.731][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.732][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:04.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:04.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.735][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:04.736][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:04.737][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.738][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.739][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:04.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:04.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:04.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:04.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:04.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:04.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.750][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:04.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:04.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:04.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:04.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:04.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:04.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.760][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:04.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:04.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:04.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:04.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.767][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:04.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:04.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:04.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:04.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.774][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:04.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:04.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:04.778][self$createEntryFromContent] Accession numbers: 139019. biodb.TRACE[2024-07-06 16:04:04.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:04.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:04.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:04.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:04.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:04.785][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:04.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:04.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:04.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:04.789][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:04.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:04.790][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:04.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:04.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:04.796][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:04.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:04.798][private$loadEntries] Creating entries from ids [1]: "139367". biodb.DEBUG[2024-07-06 16:04:04.799][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:04:04.800][cch$loadFileContent] Trying to load 1 files from cache: [1]: "139367". biodb.TRACE[2024-07-06 16:04:04.801][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:04:04.802][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:04:04.803][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:04:04.804][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:04:04.805][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:04:04.806][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:04:04.808][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:04.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:04.810][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:04.814][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:04.814][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:04.815][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:04.816][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:04.817][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=139367". biodb.DEBUG[2024-07-06 16:04:04.819][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:04:04.820][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:04:04.821][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=139367". biodb.TRACE[2024-07-06 16:04:05.224][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=139367). biodb.DEBUG[2024-07-06 16:04:05.616][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:04:05.618][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ad7d38680a9a89d96fe967aa23d4180d.content" biodb.TRACE[2024-07-06 16:04:05.621][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ad7d38680a9a89d96fe967aa23d4180d.request" biodb.TRACE[2024-07-06 16:04:05.623][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/139367.xml" biodb.DEBUG[2024-07-06 16:04:05.624][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:04:05.625][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:04:05.626][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:04:05.627][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:05.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:05.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:05.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:05.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:05.635][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:05.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:05.638][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:05.638][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:05.639][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.640][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:05.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:05.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.645][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:05.646][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:05.647][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.648][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.649][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:05.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:05.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.652][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:05.653][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:05.654][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.655][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.656][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:05.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:05.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.659][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.660][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:05.660][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:05.661][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.662][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:05.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:05.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.667][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:05.668][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:05.669][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.669][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.670][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:05.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:05.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.674][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:05.675][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:05.676][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.677][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.678][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:05.679][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:05.680][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.680][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.682][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:05.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:05.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.685][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:05.686][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:05.687][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.688][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:05.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:05.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.692][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:05.693][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:05.694][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.695][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:05.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:05.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.700][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:05.701][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:05.702][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.703][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.704][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:05.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:05.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.707][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:05.708][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:05.709][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.710][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.711][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:05.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:05.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:05.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:05.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.718][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:05.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:05.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:05.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:05.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:05.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:05.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:05.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:05.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.732][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:05.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:05.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:05.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:05.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:05.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:05.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:05.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:05.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:05.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:05.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:05.750][self$createEntryFromContent] Accession numbers: 139367. biodb.TRACE[2024-07-06 16:04:05.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:05.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:05.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.755][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:05.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:05.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:05.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:05.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:05.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:05.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:05.762][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:05.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:05.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:05.767][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:05.768][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:05.769][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:05.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:05.771][private$loadEntries] Creating entries from ids [1]: "145029". biodb.DEBUG[2024-07-06 16:04:05.772][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:04:05.773][cch$loadFileContent] Trying to load 1 files from cache: [1]: "145029". biodb.TRACE[2024-07-06 16:04:05.774][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:04:05.775][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:04:05.776][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:04:05.777][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:04:05.778][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:04:05.779][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:04:05.781][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:05.782][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:05.783][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:05.787][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:05.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:05.789][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:05.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:05.799][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=145029". biodb.DEBUG[2024-07-06 16:04:05.801][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:04:05.802][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:04:05.803][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=145029". biodb.TRACE[2024-07-06 16:04:06.190][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=145029). biodb.DEBUG[2024-07-06 16:04:06.695][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:04:06.697][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6db4642c7bdbd10dc105b3470394caa5.content" biodb.TRACE[2024-07-06 16:04:06.700][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/6db4642c7bdbd10dc105b3470394caa5.request" biodb.TRACE[2024-07-06 16:04:06.702][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/145029.xml" biodb.DEBUG[2024-07-06 16:04:06.703][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:04:06.704][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:04:06.705][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:04:06.706][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:06.707][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:06.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:06.712][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:06.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:06.714][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:06.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:06.717][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:06.718][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:06.718][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.719][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:06.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:06.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.724][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:06.725][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:06.726][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.727][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.728][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:06.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:06.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.731][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:06.732][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:06.733][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.734][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.735][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:06.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:06.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.739][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:06.740][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:06.741][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.741][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:06.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:06.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.746][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:06.747][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:06.748][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.749][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:06.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:06.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.753][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:06.754][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:06.755][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.756][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.757][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:06.758][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:06.759][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.760][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.761][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:06.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:06.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.764][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:06.765][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:06.766][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.767][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:06.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:06.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.771][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:06.772][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:06.773][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.774][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.775][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:06.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:06.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.779][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:06.780][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:06.781][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.781][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.782][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:06.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:06.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.786][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:06.787][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:06.788][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.789][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.790][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:06.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:06.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:06.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:06.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.797][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:06.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:06.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:06.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:06.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.804][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:06.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:06.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.806][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.807][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:06.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:06.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.811][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:06.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:06.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:06.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:06.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:06.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:06.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:06.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:06.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:06.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:06.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:06.829][self$createEntryFromContent] Accession numbers: 145029. biodb.TRACE[2024-07-06 16:04:06.830][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:06.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:06.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.834][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:06.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:06.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:06.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:06.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:06.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:06.840][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:06.841][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:06.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:06.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:06.846][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:06.847][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:06.848][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:06.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:06.850][private$loadEntries] Creating entries from ids [1]: "173077". biodb.DEBUG[2024-07-06 16:04:06.851][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:04:06.852][cch$loadFileContent] Trying to load 1 files from cache: [1]: "173077". biodb.TRACE[2024-07-06 16:04:06.853][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:04:06.854][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:04:06.855][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:04:06.856][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:04:06.857][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:04:06.858][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:04:06.860][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:06.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:06.862][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:06.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:06.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:06.867][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:06.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:06.869][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=173077". biodb.DEBUG[2024-07-06 16:04:06.872][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:04:06.872][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:04:06.874][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=173077". biodb.TRACE[2024-07-06 16:04:07.261][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=173077). biodb.DEBUG[2024-07-06 16:04:07.808][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:04:07.810][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/337fedbe654250105ac3b03683794b9b.content" biodb.TRACE[2024-07-06 16:04:07.813][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/337fedbe654250105ac3b03683794b9b.request" biodb.TRACE[2024-07-06 16:04:07.815][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/173077.xml" biodb.DEBUG[2024-07-06 16:04:07.816][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:04:07.817][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:04:07.818][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:04:07.820][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:07.820][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:07.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:07.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:07.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:07.827][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:07.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:07.830][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:07.831][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:07.832][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.833][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:07.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:07.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.837][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:07.838][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:07.839][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.840][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.841][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:07.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:07.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.845][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:07.846][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:07.847][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.847][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.849][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:07.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:07.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.852][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:07.853][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:07.854][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.855][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.856][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:07.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:07.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.860][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:07.860][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:07.861][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.862][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.863][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:07.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:07.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.867][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:07.868][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:07.869][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.869][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.871][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:07.872][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:07.872][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.873][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.874][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:07.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:07.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.878][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:07.879][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:07.880][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.881][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:07.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:07.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.884][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.885][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:07.886][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:07.887][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.888][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.889][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:07.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:07.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.893][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:07.894][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:07.895][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.895][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.896][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:07.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:07.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.905][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:07.912][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:07.913][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.914][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.915][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:07.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:07.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.919][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:07.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:07.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.922][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:07.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:07.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.926][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:07.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:07.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.929][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:07.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:07.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:07.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:07.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:07.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:07.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:07.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:07.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:07.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:07.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.947][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:07.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:07.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:07.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:07.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:07.954][self$createEntryFromContent] Accession numbers: 173077. biodb.TRACE[2024-07-06 16:04:07.955][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:07.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:07.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.959][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:07.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:07.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:07.962][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:07.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:07.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:07.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:07.966][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:07.966][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:07.967][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:07.971][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:07.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:07.973][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:07.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:07.975][private$loadEntries] Creating entries from ids [1]: "365445". biodb.DEBUG[2024-07-06 16:04:07.976][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:04:07.977][cch$loadFileContent] Trying to load 1 files from cache: [1]: "365445". biodb.TRACE[2024-07-06 16:04:07.978][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:04:07.979][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:04:07.980][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:04:07.981][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:04:07.982][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:04:07.983][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:04:07.985][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:07.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:07.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:07.991][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:07.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:07.992][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:07.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:07.994][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=365445". biodb.DEBUG[2024-07-06 16:04:07.997][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:04:07.997][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:04:07.999][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=365445". biodb.TRACE[2024-07-06 16:04:08.390][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=365445). biodb.DEBUG[2024-07-06 16:04:08.775][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:04:08.777][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/026ecb4be6491f40bcefe5cdf8425328.content" biodb.TRACE[2024-07-06 16:04:08.780][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/026ecb4be6491f40bcefe5cdf8425328.request" biodb.TRACE[2024-07-06 16:04:08.782][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/365445.xml" biodb.DEBUG[2024-07-06 16:04:08.783][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:04:08.784][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:04:08.785][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:04:08.787][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:08.787][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:08.788][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:08.792][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:08.793][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:08.794][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:08.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:08.796][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:08.797][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:08.798][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.799][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:08.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:08.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.804][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:08.805][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:08.806][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.806][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.807][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:08.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:08.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.811][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:08.812][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:08.813][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.814][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.815][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:08.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:08.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.819][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:08.819][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:08.820][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.821][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.822][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:08.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:08.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.826][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:08.827][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:08.828][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.829][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.830][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:08.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:08.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.833][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:08.834][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:08.835][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.836][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.837][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:08.838][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:08.839][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.839][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.841][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:08.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:08.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.844][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:08.845][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:08.846][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.847][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:08.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:08.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.851][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:08.852][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:08.853][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.854][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.855][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:08.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:08.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.859][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:08.860][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:08.861][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.861][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.863][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:08.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:08.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.866][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:08.867][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:08.868][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.869][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.870][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:08.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:08.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.874][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:08.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:08.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.876][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.877][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:08.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:08.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:08.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:08.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.884][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:08.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:08.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:08.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:08.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.891][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:08.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:08.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.895][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:08.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:08.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:08.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:08.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.902][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:08.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:08.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:08.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:08.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.908][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:08.909][self$createEntryFromContent] Accession numbers: 365445. biodb.TRACE[2024-07-06 16:04:08.910][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:08.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:08.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:08.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:08.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:08.917][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:08.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:08.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:08.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:08.921][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:08.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:08.922][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:08.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:08.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:08.928][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:08.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:08.930][private$loadEntries] Creating entries from ids [1]: "32151". biodb.DEBUG[2024-07-06 16:04:08.931][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:04:08.932][cch$loadFileContent] Trying to load 1 files from cache: [1]: "32151". biodb.TRACE[2024-07-06 16:04:08.933][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:04:08.934][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:04:08.935][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:04:08.936][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:04:08.937][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:04:08.938][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:04:08.941][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:08.941][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:08.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:08.946][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:08.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:08.948][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:08.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:08.950][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=32151". biodb.DEBUG[2024-07-06 16:04:08.952][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:04:08.953][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:04:08.954][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=32151". biodb.TRACE[2024-07-06 16:04:09.358][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=32151). biodb.DEBUG[2024-07-06 16:04:09.744][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:04:09.746][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/094c4c16dd654c0e11594a0cd5a42217.content" biodb.TRACE[2024-07-06 16:04:09.748][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/094c4c16dd654c0e11594a0cd5a42217.request" biodb.TRACE[2024-07-06 16:04:09.751][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32151.xml" biodb.DEBUG[2024-07-06 16:04:09.752][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:04:09.763][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:04:09.765][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:04:09.766][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:09.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:09.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:09.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:09.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:09.774][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:09.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:09.777][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:09.778][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:09.779][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.779][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:09.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:09.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.784][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:09.785][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:09.786][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.787][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.788][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:09.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:09.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.791][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:09.792][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:09.793][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.794][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.795][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:09.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:09.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.799][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:09.800][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:09.801][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.801][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.803][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:09.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:09.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.806][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:09.807][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:09.808][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.809][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.810][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:09.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:09.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.813][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:09.814][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:09.815][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.816][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.817][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:09.818][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:09.819][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.820][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.821][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:09.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:09.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.824][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:09.825][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:09.826][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.827][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:09.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:09.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.832][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:09.833][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:09.833][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.834][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.835][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:09.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:09.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.839][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:09.840][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:09.841][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.841][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.843][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:09.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:09.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.846][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:09.847][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:09.848][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.849][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.850][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:09.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:09.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:09.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:09.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.857][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:09.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:09.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:09.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:09.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.863][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:09.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:09.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:09.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:09.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:09.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:09.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:09.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:09.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:09.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:09.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.881][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:09.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:09.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.884][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:09.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:09.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:09.889][self$createEntryFromContent] Accession numbers: 32151. biodb.TRACE[2024-07-06 16:04:09.890][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:09.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:09.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:09.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:09.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.896][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:09.897][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:09.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:09.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:09.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:09.900][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:09.901][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:09.902][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:09.906][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:09.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:09.908][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:09.908][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:09.909][private$loadEntries] Creating entries from ids [1]: "67676". biodb.DEBUG[2024-07-06 16:04:09.910][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:04:09.912][cch$loadFileContent] Trying to load 1 files from cache: [1]: "67676". biodb.TRACE[2024-07-06 16:04:09.913][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:04:09.914][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:04:09.915][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:04:09.916][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:04:09.917][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:04:09.917][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:04:09.920][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:09.921][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:09.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:09.925][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:09.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:09.927][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:09.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:09.929][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67676". biodb.DEBUG[2024-07-06 16:04:09.931][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:04:09.932][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:04:09.934][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67676". biodb.TRACE[2024-07-06 16:04:10.342][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=67676). biodb.DEBUG[2024-07-06 16:04:10.732][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:04:10.734][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f87eff9f669415e5528b4d9281ce70e2.content" biodb.TRACE[2024-07-06 16:04:10.737][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f87eff9f669415e5528b4d9281ce70e2.request" biodb.TRACE[2024-07-06 16:04:10.739][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/67676.xml" biodb.DEBUG[2024-07-06 16:04:10.740][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:04:10.742][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:04:10.743][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:04:10.744][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:10.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:10.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:10.750][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:10.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:10.751][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:10.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:10.754][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:10.755][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:10.756][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.757][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:10.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:10.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.761][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:10.762][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:10.763][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.764][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.765][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:10.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:10.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.769][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:10.770][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:10.771][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.771][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.772][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:10.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:10.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.776][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:10.777][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:10.778][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.779][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.780][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:10.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:10.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.783][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:10.784][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:10.785][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.786][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.787][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:10.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:10.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.791][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:10.792][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:10.792][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.793][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.794][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:10.795][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:10.796][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.797][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.798][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:10.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:10.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.802][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:10.803][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:10.803][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.804][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:10.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:10.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.809][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:10.810][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:10.811][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.812][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.813][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:10.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:10.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.816][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:10.817][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:10.818][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.819][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.820][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:10.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:10.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.824][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:10.825][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:10.825][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.826][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.827][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:10.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:10.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.831][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:10.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:10.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.835][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:10.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:10.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:10.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:10.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:10.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:10.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:10.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:10.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:10.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:10.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.860][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:10.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:10.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.863][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:10.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:10.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.867][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:10.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:10.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:10.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:10.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:10.875][self$createEntryFromContent] Accession numbers: 67676. biodb.TRACE[2024-07-06 16:04:10.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:10.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:10.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.878][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.879][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:10.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:10.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:10.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:10.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:10.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:10.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:10.886][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:10.887][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:10.888][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:10.891][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:10.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:10.893][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:10.894][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:10.895][private$loadEntries] Creating entries from ids [1]: "69690". biodb.DEBUG[2024-07-06 16:04:10.896][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:04:10.897][cch$loadFileContent] Trying to load 1 files from cache: [1]: "69690". biodb.TRACE[2024-07-06 16:04:10.898][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:04:10.899][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:04:10.900][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:04:10.901][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:04:10.902][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:04:10.903][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:04:10.905][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:10.906][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:10.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:10.910][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:10.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:10.912][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:10.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:10.914][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69690". biodb.DEBUG[2024-07-06 16:04:10.916][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:04:10.917][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:04:10.918][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69690". biodb.TRACE[2024-07-06 16:04:11.524][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69690). biodb.DEBUG[2024-07-06 16:04:11.912][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:04:11.914][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4ce43467f7e4550d502ff0cc79c06666.content" biodb.TRACE[2024-07-06 16:04:11.917][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4ce43467f7e4550d502ff0cc79c06666.request" biodb.TRACE[2024-07-06 16:04:11.919][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/69690.xml" biodb.DEBUG[2024-07-06 16:04:11.920][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:04:11.921][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:04:11.922][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:04:11.924][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:11.924][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:11.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:11.929][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:11.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:11.931][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:11.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:11.934][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:11.935][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:11.935][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.936][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:11.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:11.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:11.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:11.941][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:11.942][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:11.943][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.944][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:11.945][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:11.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:11.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:11.948][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:11.949][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:11.950][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.951][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:11.952][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:11.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:11.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:11.956][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:11.956][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:11.957][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.958][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:11.959][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:11.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:11.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:11.963][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:11.964][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:11.965][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.966][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:11.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:11.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:11.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:11.970][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:11.971][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:11.972][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.973][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:11.974][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:11.975][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:11.976][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.977][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:11.978][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:11.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:11.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:11.981][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:11.982][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:11.983][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.984][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:11.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:11.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:11.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:11.989][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:11.990][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:11.991][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.991][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:11.993][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:11.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:11.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:11.996][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:11.997][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:11.998][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:11.999][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.000][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:12.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:12.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.004][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:12.005][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:12.006][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.006][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.008][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:12.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:12.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.010][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.011][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:12.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:12.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:12.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:12.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:12.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:12.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.022][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:12.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:12.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:12.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:12.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:12.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:12.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:12.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:12.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:12.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:12.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:12.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:12.041][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.043][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:12.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:12.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:12.047][self$createEntryFromContent] Accession numbers: 69690. biodb.TRACE[2024-07-06 16:04:12.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:12.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:12.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:12.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:12.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:12.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:12.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:12.058][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:12.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:12.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:12.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:12.065][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:12.065][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:12.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:12.067][private$loadEntries] Creating entries from ids [1]: "69734". biodb.DEBUG[2024-07-06 16:04:12.068][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:04:12.070][cch$loadFileContent] Trying to load 1 files from cache: [1]: "69734". biodb.TRACE[2024-07-06 16:04:12.071][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:04:12.072][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:04:12.073][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:04:12.074][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:04:12.074][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:04:12.075][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:04:12.078][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:12.078][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:12.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:12.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:12.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:12.085][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:12.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:12.087][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69734". biodb.DEBUG[2024-07-06 16:04:12.089][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:04:12.090][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:04:12.091][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69734". biodb.TRACE[2024-07-06 16:04:12.487][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=69734). biodb.DEBUG[2024-07-06 16:04:12.895][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:04:12.897][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/3ed7db8dba94801a8856f9bde313afe1.content" biodb.TRACE[2024-07-06 16:04:12.900][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/3ed7db8dba94801a8856f9bde313afe1.request" biodb.TRACE[2024-07-06 16:04:12.902][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/69734.xml" biodb.DEBUG[2024-07-06 16:04:12.903][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:04:12.904][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:04:12.905][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:04:12.907][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:12.908][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:12.909][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:12.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:12.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:12.914][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:12.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:12.917][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:12.918][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:12.919][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.920][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:12.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:12.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.936][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:12.937][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:12.937][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.938][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.939][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:12.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:12.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.943][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:12.944][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:12.945][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.946][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.947][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:12.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:12.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.950][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:12.951][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:12.952][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.953][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.954][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:12.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:12.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.958][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:12.959][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:12.959][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.960][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.961][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:12.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:12.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.965][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:12.966][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:12.967][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.968][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.969][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:12.970][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:12.970][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.971][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.972][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:12.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:12.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.976][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:12.977][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:12.978][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.979][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:12.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:12.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.983][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:12.984][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:12.985][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.986][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.987][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:12.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:12.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.991][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:12.992][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:12.993][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.994][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.995][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:12.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:12.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:12.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:12.998][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:12.999][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:13.000][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.001][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.002][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:13.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:13.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:13.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:13.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:13.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:13.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.013][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:13.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:13.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:13.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:13.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:13.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:13.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:13.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:13.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.027][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:13.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:13.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:13.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:13.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:13.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:13.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:13.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:13.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:13.041][self$createEntryFromContent] Accession numbers: 69734. biodb.TRACE[2024-07-06 16:04:13.042][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:13.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:13.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:13.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:13.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:13.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:13.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:13.053][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:13.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:13.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:13.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:13.059][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:13.060][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:13.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:13.062][private$loadEntries] Creating entries from ids [1]: "79978". biodb.DEBUG[2024-07-06 16:04:13.063][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:04:13.064][cch$loadFileContent] Trying to load 1 files from cache: [1]: "79978". biodb.TRACE[2024-07-06 16:04:13.066][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:04:13.067][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:04:13.068][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:04:13.069][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:04:13.069][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:04:13.070][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:04:13.073][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:13.073][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:13.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:13.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:13.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:13.080][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:13.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:13.082][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79978". biodb.DEBUG[2024-07-06 16:04:13.084][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:04:13.085][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:04:13.087][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79978". biodb.TRACE[2024-07-06 16:04:13.478][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=79978). biodb.DEBUG[2024-07-06 16:04:13.862][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:04:13.864][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/fb887d003d6fc3b4aa767483d261b31c.content" biodb.TRACE[2024-07-06 16:04:13.867][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/fb887d003d6fc3b4aa767483d261b31c.request" biodb.TRACE[2024-07-06 16:04:13.869][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/79978.xml" biodb.DEBUG[2024-07-06 16:04:13.871][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:04:13.872][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:04:13.873][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:04:13.874][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:13.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:13.876][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:13.880][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:13.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:13.881][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:13.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:13.884][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:13.885][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:13.886][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.887][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:13.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:13.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.892][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:13.892][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:13.893][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.894][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.895][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:13.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:13.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.899][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:13.900][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:13.901][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.902][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.903][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:13.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:13.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.906][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:13.907][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:13.908][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.909][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.910][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:13.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:13.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.914][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:13.915][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:13.915][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.916][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.917][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:13.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:13.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.921][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:13.922][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:13.923][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.924][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.925][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:13.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:13.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.928][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:13.929][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:13.930][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.931][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.932][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:13.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:13.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.936][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:13.937][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:13.937][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.938][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.939][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:13.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:13.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.943][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:13.944][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:13.945][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.946][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:13.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:13.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.951][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:13.951][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:13.952][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.953][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.954][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:13.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:13.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.958][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:13.959][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:13.960][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.960][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.962][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:13.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:13.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:13.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:13.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.969][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:13.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:13.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.972][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:13.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:13.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.975][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.976][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:13.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:13.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.979][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:13.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:13.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.983][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:13.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:13.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.995][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:13.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:13.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:13.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:13.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:14.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:14.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:14.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:14.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:14.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:14.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:14.009][self$createEntryFromContent] Accession numbers: 79978. biodb.TRACE[2024-07-06 16:04:14.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.013][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.014][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:14.021][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:14.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:14.022][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:14.026][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:14.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:14.028][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:14.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:14.029][private$loadEntries] Creating entries from ids [1]: "88771". biodb.DEBUG[2024-07-06 16:04:14.030][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)... biodb.TRACE[2024-07-06 16:04:14.032][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88771". biodb.TRACE[2024-07-06 16:04:14.033][cch$loadFileContent] file.exist = [1]: "FALSE". biodb.TRACE[2024-07-06 16:04:14.034][loadFileContents] Loaded 0 files from cache: none. biodb.DEBUG[2024-07-06 16:04:14.035][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache. biodb.DEBUG[2024-07-06 16:04:14.036][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/". biodb.DEBUG[2024-07-06 16:04:14.037][conn$getEntryContent] dwnld.chunk.size=NA biodb.DEBUG[2024-07-06 16:04:14.037][conn$getEntryContent] 1 chunk(s) to download. biodb.DEBUG[2024-07-06 16:04:14.040][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:14.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:14.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:14.045][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:14.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:14.047][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:14.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:14.049][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88771". biodb.DEBUG[2024-07-06 16:04:14.051][private$doSendRequestLoop] Request header is: "". biodb.DEBUG[2024-07-06 16:04:14.052][private$doSendRequestLoop] Request body is "". biodb.TRACE[2024-07-06 16:04:14.053][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88771". biodb.TRACE[2024-07-06 16:04:14.449][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88771). biodb.DEBUG[2024-07-06 16:04:14.836][scheduler$sendRequest] Saving content of request to cache. biodb.TRACE[2024-07-06 16:04:14.838][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f96325cdb7f39b42d0ab67a7fc41aced.content" biodb.TRACE[2024-07-06 16:04:14.841][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f96325cdb7f39b42d0ab67a7fc41aced.request" biodb.TRACE[2024-07-06 16:04:14.843][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88771.xml" biodb.DEBUG[2024-07-06 16:04:14.844][conn$getEntryContent] Now 0 id(s) left to be retrieved... biodb.DEBUG[2024-07-06 16:04:14.845][self$createEntryFromContent] Creating ChEBI entries from 1 content(s). biodb.DEBUG[2024-07-06 16:04:14.846][self$createEntryFromContent] Parsing 1 ChEBI entries. biodb.DEBUG[2024-07-06 16:04:14.847][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:14.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:14.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:14.853][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:14.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:14.855][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:14.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:14.857][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:14.858][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:14.859][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.860][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.861][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:14.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:14.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.865][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:14.865][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:14.866][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.867][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.868][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:14.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:14.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.872][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:14.873][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:14.874][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.874][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.876][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:14.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:14.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.878][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.879][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:14.880][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:14.881][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.882][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.883][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:14.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:14.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.886][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:14.887][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:14.888][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.889][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.890][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:14.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:14.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.893][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.894][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:14.894][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:14.895][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.896][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.897][ef$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:14.898][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:14.899][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.900][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.901][self$getBiodb()$getEntryFields()$get] Asked field names are: mass. biodb.TRACE[2024-07-06 16:04:14.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:14.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.905][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.906][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.906][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.907][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.912][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:14.913][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:14.914][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.915][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.916][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:14.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:14.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.919][ef$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:14.920][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:14.921][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.922][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.923][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars. biodb.TRACE[2024-07-06 16:04:14.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:14.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.927][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:14.928][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:14.928][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.929][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.930][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:14.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:14.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:14.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:14.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.937][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:14.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:14.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:14.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:14.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.944][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:14.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:14.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:14.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:14.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:14.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:14.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:14.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:14.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:14.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:14.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:14.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:14.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:14.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:14.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:14.969][self$createEntryFromContent] Accession numbers: 88771. biodb.TRACE[2024-07-06 16:04:14.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.974][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.977][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.977][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:14.981][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:14.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:14.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:14.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:14.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:14.988][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:14.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:14.990][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.994][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:14.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:14.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:14.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:15.001][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.006][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.008][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.010][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:15.020][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:15.022][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.023][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.027][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.029][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.031][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.038][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.039][private$selectFields] biodb.TRACE[2024-07-06 16:04:15.040][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:15.040][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:15.041][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.042][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.043][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.044][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.045][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.046][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.047][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.048][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.048][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.049][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.050][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.059][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.060][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.061][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.062][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.063][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:15.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.067][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.074][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.075][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-07-06 16:04:15.076][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.076][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.081][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.082][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.083][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.085][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.088][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.092][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.092][private$selectFields] biodb.TRACE[2024-07-06 16:04:15.093][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:15.094][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:15.095][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.096][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.097][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.097][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.098][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.099][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.100][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.101][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.102][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.103][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.104][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.104][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.105][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.106][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.107][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.108][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:15.109][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.111][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.112][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.116][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.119][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [91601]. biodb.DEBUG[2024-07-06 16:04:15.120][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.126][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.127][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.129][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.136][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.137][private$selectFields] biodb.TRACE[2024-07-06 16:04:15.138][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:15.139][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:15.140][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.140][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.141][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.142][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.143][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.144][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.145][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.146][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.146][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.147][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.148][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.149][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.150][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.151][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.152][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.153][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:15.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.164][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [95147]. biodb.DEBUG[2024-07-06 16:04:15.165][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:15.166][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:15.168][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.169][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.169][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.173][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.175][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:15.178][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:15.181][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:15.182][cch$loadFileContent] Trying to load 1 files from cache: [1]: "a035d13a630066423fab6713592c5e52". biodb.TRACE[2024-07-06 16:04:15.183][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:15.185][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a035d13a630066423fab6713592c5e52.content". biodb.DEBUG[2024-07-06 16:04:15.190][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.196][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.197][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.206][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:15.210][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.210][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.211][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.217][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.218][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.226][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:15.229][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.230][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.231][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.236][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:15.249][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.250][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.254][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.256][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.257][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.258][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.265][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:15.269][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:15.270][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.271][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.277][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.279][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.283][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.286][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.287][private$selectFields] biodb.TRACE[2024-07-06 16:04:15.288][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:15.289][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:15.290][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.291][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.292][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.293][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.293][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.294][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.295][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.296][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.297][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.298][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.299][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.300][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.301][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.302][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.302][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.303][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:15.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.316][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [636]. biodb.DEBUG[2024-07-06 16:04:15.317][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.318][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.318][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.323][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.324][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.326][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.333][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.334][private$selectFields] biodb.TRACE[2024-07-06 16:04:15.335][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:15.336][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:15.341][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.343][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.344][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.345][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.346][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.347][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.348][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.349][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.350][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.351][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.352][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.353][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.354][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.354][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.355][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.356][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:15.357][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.361][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.364][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.368][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [3014]. biodb.DEBUG[2024-07-06 16:04:15.369][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.370][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.370][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.374][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.376][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.385][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.386][private$selectFields] biodb.TRACE[2024-07-06 16:04:15.387][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:15.387][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:15.388][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.389][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.390][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.391][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.392][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.392][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.393][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.394][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.395][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.396][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.397][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.398][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.399][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.399][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.400][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.401][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:15.402][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.405][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.409][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.413][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-07-06 16:04:15.414][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:15.414][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:15.430][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.431][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.432][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.437][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:15.440][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:15.443][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:15.444][cch$loadFileContent] Trying to load 1 files from cache: [1]: "a035d13a630066423fab6713592c5e52". biodb.TRACE[2024-07-06 16:04:15.445][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:15.447][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a035d13a630066423fab6713592c5e52.content". biodb.DEBUG[2024-07-06 16:04:15.452][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.453][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.459][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:15.471][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.478][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.478][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.486][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.487][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:15.491][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.496][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.498][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.500][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.506][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:15.511][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.516][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.518][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.529][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:15.530][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.536][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.536][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.537][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.539][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.546][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:15.550][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.550][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.557][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.561][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.562][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:15.569][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.571][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.575][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.576][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.582][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.585][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:15.589][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:15.590][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.591][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.596][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.597][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.597][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.603][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.607][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.607][private$selectFields] biodb.TRACE[2024-07-06 16:04:15.608][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:15.609][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:15.610][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.611][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.612][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.613][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.614][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.615][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.615][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.616][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.617][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.618][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.625][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.626][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.627][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.628][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.628][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.629][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:15.630][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.636][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.641][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [3014]. biodb.DEBUG[2024-07-06 16:04:15.642][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.649][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.651][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.654][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.657][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.658][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.658][private$selectFields] biodb.TRACE[2024-07-06 16:04:15.659][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:15.660][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:15.661][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.662][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.663][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.664][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.664][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.665][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.666][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.667][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.668][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.669][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.670][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.671][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.671][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.672][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.673][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.674][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:15.675][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.678][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.682][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.686][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-07-06 16:04:15.687][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.687][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.692][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.693][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.694][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.694][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.695][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.699][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.702][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.702][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.703][private$selectFields] biodb.TRACE[2024-07-06 16:04:15.704][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:15.705][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:15.706][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.707][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.708][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.708][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.709][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.710][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.711][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.712][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.713][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.714][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.714][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.715][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.716][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.717][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.718][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.719][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:15.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.727][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.729][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.730][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [34764]. biodb.DEBUG[2024-07-06 16:04:15.731][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:15.732][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:15.734][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.741][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:15.744][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:15.747][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:15.748][cch$loadFileContent] Trying to load 1 files from cache: [1]: "365d4ea5e0e90826806fec708da6c9ab". biodb.TRACE[2024-07-06 16:04:15.749][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:15.751][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/365d4ea5e0e90826806fec708da6c9ab.content". biodb.DEBUG[2024-07-06 16:04:15.757][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.758][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.763][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.764][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.766][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.770][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.773][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:15.777][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.782][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.784][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.793][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:15.797][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.798][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.798][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.804][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.805][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.806][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.809][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.813][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:15.816][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.822][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.823][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.824][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.824][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.829][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:15.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:15.836][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:15.838][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.838][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.839][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.843][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.845][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.854][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.855][private$selectFields] biodb.TRACE[2024-07-06 16:04:15.855][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:15.856][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:15.857][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.858][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.859][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.860][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.861][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.862][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.863][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.863][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.864][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.865][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.866][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.867][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.868][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.869][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.870][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.870][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:15.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.875][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.878][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.881][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.882][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [2535]. biodb.DEBUG[2024-07-06 16:04:15.883][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.884][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.889][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.890][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.890][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.900][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.900][private$selectFields] biodb.TRACE[2024-07-06 16:04:15.907][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:15.908][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:15.909][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.910][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.911][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.912][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.912][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.913][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.914][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.915][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.916][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.917][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.918][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.918][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.919][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.920][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.921][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.922][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:15.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.926][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.933][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-07-06 16:04:15.934][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.940][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.941][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:15.943][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.950][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.951][private$selectFields] biodb.TRACE[2024-07-06 16:04:15.952][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:15.953][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:15.954][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.954][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.955][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.956][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.957][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.958][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.959][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.960][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.960][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.961][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.962][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:15.963][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.964][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.965][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.966][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.966][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:15.967][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.971][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:15.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:15.977][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:15.978][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [16587]. biodb.DEBUG[2024-07-06 16:04:15.979][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:15.980][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:15.981][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:15.982][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:15.983][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:15.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:15.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:15.988][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:15.989][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:15.992][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=409.9*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:15.994][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:15.995][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7b0416ab2d5cbf869f248000c039a8e8". biodb.TRACE[2024-07-06 16:04:15.997][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:15.998][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7b0416ab2d5cbf869f248000c039a8e8.content". biodb.DEBUG[2024-07-06 16:04:16.000][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.001][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.005][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.007][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.009][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:16.019][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.020][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.025][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.026][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.031][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.032][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.038][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:16.039][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.044][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.046][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.048][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.055][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:16.058][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.059][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.060][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.064][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.065][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.070][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:16.078][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.078][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.079][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.085][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.085][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.086][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.093][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:16.097][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:16.099][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.099][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.104][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.105][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.106][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.107][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.115][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.115][private$selectFields] biodb.TRACE[2024-07-06 16:04:16.116][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:16.117][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:16.118][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.119][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.120][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.121][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.121][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.122][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.123][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.124][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.125][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.126][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.127][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.128][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.129][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.129][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.130][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.131][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:16.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.142][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.143][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [31303]. biodb.DEBUG[2024-07-06 16:04:16.144][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.145][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.149][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.151][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.153][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.156][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.160][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.161][private$selectFields] biodb.TRACE[2024-07-06 16:04:16.162][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:16.162][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:16.163][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.164][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.165][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.166][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.167][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.168][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.169][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.169][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.170][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.171][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.172][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.173][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.174][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.175][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.176][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.177][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:16.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.190][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.194][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [81767]. biodb.DEBUG[2024-07-06 16:04:16.195][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.200][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.202][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.204][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.206][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.210][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.211][private$selectFields] biodb.TRACE[2024-07-06 16:04:16.212][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:16.213][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:16.214][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.215][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.216][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.216][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.217][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.218][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.219][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.220][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.221][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.222][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.222][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.223][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.224][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.225][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.226][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.227][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:16.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.231][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.238][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [131378]. biodb.DEBUG[2024-07-06 16:04:16.239][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:16.240][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:16.256][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.257][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.261][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.262][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.262][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:16.266][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:16.268][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:16.269][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2024-07-06 16:04:16.271][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:16.272][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2024-07-06 16:04:16.274][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:16.277][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:16.278][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2024-07-06 16:04:16.279][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:16.280][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2024-07-06 16:04:16.282][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.283][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.289][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.297][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:16.302][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.302][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.307][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.308][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.314][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.317][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:16.321][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.322][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.327][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.328][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.330][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.337][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:16.341][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:16.342][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.343][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.349][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.351][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.354][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.358][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.359][private$selectFields] biodb.TRACE[2024-07-06 16:04:16.359][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:16.360][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:16.361][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.362][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.363][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.364][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.365][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.366][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.366][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.367][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.368][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.369][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.370][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.371][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.372][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.373][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.373][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.374][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:16.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.379][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.382][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.386][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2024-07-06 16:04:16.387][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.392][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.393][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.394][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.403][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.404][private$selectFields] biodb.TRACE[2024-07-06 16:04:16.405][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:16.405][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:16.406][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.407][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.408][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.409][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.410][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.411][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.412][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.413][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.413][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.414][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.415][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.416][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.417][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.418][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.419][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.420][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:16.420][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.424][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.427][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.430][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.431][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-07-06 16:04:16.432][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.434][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.438][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.439][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.448][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.449][private$selectFields] biodb.TRACE[2024-07-06 16:04:16.450][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:16.451][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:16.452][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.453][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.454][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.454][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.455][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.456][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.457][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.458][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.481][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.483][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.483][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.484][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.485][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.486][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.487][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.488][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:16.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.491][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.492][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.496][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.498][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.500][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2024-07-06 16:04:16.500][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:16.501][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:16.503][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.510][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:16.513][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.29*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:16.516][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:16.517][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7269bbea581f1e243800f8ee4e0f4fdb". biodb.TRACE[2024-07-06 16:04:16.518][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:16.519][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7269bbea581f1e243800f8ee4e0f4fdb.content". biodb.DEBUG[2024-07-06 16:04:16.522][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.522][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.527][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.528][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.529][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.534][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.538][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:16.541][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.547][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.548][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.550][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:16.561][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.561][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.562][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.566][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.567][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.567][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.569][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:16.580][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:16.581][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.582][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.583][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.587][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.588][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.588][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.589][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.594][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.597][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.598][private$selectFields] biodb.TRACE[2024-07-06 16:04:16.599][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:16.600][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:16.601][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.602][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.603][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.604][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.604][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.605][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.606][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.607][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.608][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.609][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.610][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.611][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.612][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.613][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.613][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.614][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:16.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.619][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.622][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.626][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-07-06 16:04:16.627][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.633][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.635][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.637][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.641][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.643][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.644][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.645][private$selectFields] biodb.TRACE[2024-07-06 16:04:16.646][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:16.647][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:16.648][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.648][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.649][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.650][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.651][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.652][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.653][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.654][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.655][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.656][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.657][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.658][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.658][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.659][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.660][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.661][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:16.662][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.668][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.673][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [91601]. biodb.DEBUG[2024-07-06 16:04:16.674][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.682][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.684][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.687][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.691][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.692][private$selectFields] biodb.TRACE[2024-07-06 16:04:16.693][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:16.693][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:16.694][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.695][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.696][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.697][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.698][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.699][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.700][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.701][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.701][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.702][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.703][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.704][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.705][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.706][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.707][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.708][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:16.709][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.711][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.712][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.715][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.716][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.720][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [95147]. biodb.DEBUG[2024-07-06 16:04:16.721][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:16.722][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:16.723][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.724][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.729][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.730][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.731][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:16.734][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:16.737][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:16.738][cch$loadFileContent] Trying to load 1 files from cache: [1]: "acfa4b558978abf12409c2b56e678d03". biodb.TRACE[2024-07-06 16:04:16.739][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:16.741][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/acfa4b558978abf12409c2b56e678d03.content". biodb.DEBUG[2024-07-06 16:04:16.744][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.744][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.751][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.760][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:16.764][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.765][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.775][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.777][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.779][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.782][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:16.789][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.790][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.791][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.795][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.797][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.804][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.805][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:16.809][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:16.810][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.811][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.812][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.817][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.819][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.823][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.826][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.827][private$selectFields] biodb.TRACE[2024-07-06 16:04:16.828][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:16.829][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:16.830][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.831][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.832][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.832][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.833][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.834][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.835][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.836][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.837][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.838][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.838][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.839][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.840][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.841][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.842][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.843][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:16.844][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.851][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.854][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [636]. biodb.DEBUG[2024-07-06 16:04:16.855][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.856][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.863][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.864][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.867][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.871][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.872][private$selectFields] biodb.TRACE[2024-07-06 16:04:16.873][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:16.874][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:16.875][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.876][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.877][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.878][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.878][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.879][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.880][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.881][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.882][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.883][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.884][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.885][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.886][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.887][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.887][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.888][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:16.889][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.893][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.896][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.900][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [64199]. biodb.DEBUG[2024-07-06 16:04:16.901][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.902][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.903][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.907][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.909][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.910][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.914][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.918][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.918][private$selectFields] biodb.TRACE[2024-07-06 16:04:16.919][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:16.920][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:16.921][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.922][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.923][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.924][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.925][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.925][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.926][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.927][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.928][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.929][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.930][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:16.931][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.932][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.933][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.933][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.934][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:16.935][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.939][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:16.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.945][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.946][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [65648]. biodb.DEBUG[2024-07-06 16:04:16.947][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:16.948][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:16.965][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.965][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.966][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.971][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:16.975][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.3*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:16.978][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:16.979][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26eec570aadd234892b573eb0777bd78". biodb.TRACE[2024-07-06 16:04:16.980][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:16.981][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26eec570aadd234892b573eb0777bd78.content". biodb.DEBUG[2024-07-06 16:04:16.984][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:16.985][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:16.986][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:16.989][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:16.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:16.991][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:16.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:16.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.996][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:16.997][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:16.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:16.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.000][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.003][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.004][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.011][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.024][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.024][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.025][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.031][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.042][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.043][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.044][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.045][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.051][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.056][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.058][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.062][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.065][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.069][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.070][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.074][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.075][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.076][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.078][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.088][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.089][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.095][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.097][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.108][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.110][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.115][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.128][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.128][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.129][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.133][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.135][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.140][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.143][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.147][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:17.149][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.149][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.150][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.154][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.155][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.156][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.157][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.161][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.164][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.165][private$selectFields] biodb.TRACE[2024-07-06 16:04:17.166][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:17.167][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:17.168][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.169][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.170][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.171][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.172][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.172][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.173][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.174][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.175][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.176][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.177][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.178][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.179][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.180][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.180][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.181][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:17.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.185][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.186][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.189][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.193][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648]. biodb.DEBUG[2024-07-06 16:04:17.194][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.195][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.196][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.200][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.201][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.201][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.203][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.206][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.207][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.210][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.211][private$selectFields] biodb.TRACE[2024-07-06 16:04:17.212][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:17.213][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:17.214][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.215][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.216][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.217][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.217][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.218][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.219][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.220][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.221][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.222][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.223][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.224][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.225][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.225][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.226][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.227][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:17.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.232][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.239][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440]. biodb.DEBUG[2024-07-06 16:04:17.240][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.247][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.249][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.253][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.256][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.257][private$selectFields] biodb.TRACE[2024-07-06 16:04:17.258][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:17.259][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:17.260][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.261][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.262][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.263][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.263][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.264][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.265][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.266][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.267][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.268][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.269][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.270][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.271][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.271][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.272][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.273][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:17.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.285][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447]. biodb.DEBUG[2024-07-06 16:04:17.286][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:17.287][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:17.289][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.289][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.290][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.296][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:17.299][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.2*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:17.302][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:17.303][cch$loadFileContent] Trying to load 1 files from cache: [1]: "20c224089a82bbffabd2e7dbc67cfae3". biodb.TRACE[2024-07-06 16:04:17.304][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:17.306][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/20c224089a82bbffabd2e7dbc67cfae3.content". biodb.DEBUG[2024-07-06 16:04:17.311][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.312][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.317][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.319][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.323][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.324][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.327][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.330][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.331][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.332][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.333][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.345][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.346][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.354][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.357][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.358][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.364][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.366][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.373][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.377][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.382][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.384][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.396][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.398][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.401][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.402][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.403][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.408][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.411][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.416][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.421][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.423][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.423][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.424][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.427][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.428][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.431][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.434][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.435][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.441][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.442][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.455][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.456][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.457][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.461][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.462][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.464][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.468][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.472][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.475][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.481][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.482][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.482][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.491][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.494][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.495][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.496][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.502][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.504][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.507][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.511][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.515][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.516][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.520][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.522][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.523][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.527][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.531][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.534][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.542][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.550][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.551][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.554][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.555][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.560][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.561][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.574][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.575][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.575][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.579][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.581][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.583][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.586][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.589][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.590][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.594][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.595][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.599][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.601][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.610][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.614][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.619][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.621][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.631][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.635][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.639][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.639][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.644][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.645][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.645][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.647][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.650][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.651][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.654][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.657][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.658][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.663][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.664][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.665][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.677][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.678][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.682][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.683][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.684][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.688][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.692][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.695][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.696][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.697][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.702][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.702][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.703][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.705][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.709][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.711][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.715][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.716][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.723][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.728][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.732][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.735][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.736][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.737][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.741][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.742][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.751][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.752][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.755][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.756][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.761][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.762][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.764][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.768][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.775][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.776][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.782][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.784][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.791][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.795][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.800][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.802][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.811][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.815][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.816][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.817][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.821][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.822][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.832][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.835][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.836][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.837][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.841][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.843][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.844][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.847][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.848][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.852][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.855][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.856][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.857][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.861][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.862][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.862][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.864][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.867][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.868][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.871][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.875][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.876][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.882][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.884][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.888][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.891][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.895][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.895][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.896][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.902][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.904][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.907][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.915][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:17.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:17.920][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:17.921][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.928][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.930][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.934][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.937][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.938][private$selectFields] biodb.TRACE[2024-07-06 16:04:17.939][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:17.940][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:17.940][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.941][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.942][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.943][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.944][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.945][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.946][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.947][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.947][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.948][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.949][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.950][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.951][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.952][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.953][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.954][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:17.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.958][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.961][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.965][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4781]. biodb.DEBUG[2024-07-06 16:04:17.966][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:17.967][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:17.968][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:17.972][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:17.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:17.973][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:17.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:17.975][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.979][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.982][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.983][private$selectFields] biodb.TRACE[2024-07-06 16:04:17.984][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:17.985][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:17.985][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.986][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.987][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.988][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.989][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.990][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.991][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.992][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.992][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.993][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.994][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:17.995][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.996][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:17.997][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:17.998][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:17.998][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:17.999][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.007][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.011][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [91601]. biodb.DEBUG[2024-07-06 16:04:18.012][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:18.012][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:18.013][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:18.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:18.018][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:18.019][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:18.020][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:18.021][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.025][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.028][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:18.029][private$selectFields] biodb.TRACE[2024-07-06 16:04:18.030][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:18.031][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:18.031][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:18.032][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.033][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.034][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.035][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.036][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.037][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.038][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.039][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.039][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:18.040][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:18.041][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.042][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.043][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.044][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.045][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:18.046][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.053][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.057][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [95147]. biodb.DEBUG[2024-07-06 16:04:18.058][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:18.058][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:18.060][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:18.061][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:18.062][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:18.066][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:18.067][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:18.067][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:18.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:18.071][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.1*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:18.074][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:18.075][cch$loadFileContent] Trying to load 1 files from cache: [1]: "a035d13a630066423fab6713592c5e52". biodb.TRACE[2024-07-06 16:04:18.076][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:18.077][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a035d13a630066423fab6713592c5e52.content". biodb.DEBUG[2024-07-06 16:04:18.083][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:18.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:18.084][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:18.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:18.089][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:18.090][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:18.091][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:18.092][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.094][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.095][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:18.103][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:18.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:18.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:18.109][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:18.109][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:18.110][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:18.111][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:18.112][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.116][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.119][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:18.123][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:18.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:18.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:18.128][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:18.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:18.130][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:18.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:18.132][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.136][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.142][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:18.143][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:18.144][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:18.144][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:18.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:18.149][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:18.150][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:18.151][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:18.152][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.155][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.159][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:18.163][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:18.164][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:18.165][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:18.166][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:18.170][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:18.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:18.171][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:18.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:18.173][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.177][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.181][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:18.181][private$selectFields] biodb.TRACE[2024-07-06 16:04:18.182][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:18.183][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:18.184][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:18.185][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.186][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.187][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.188][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.188][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.189][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.190][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.191][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.192][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:18.193][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:18.200][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.201][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.202][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.203][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.204][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:18.205][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.208][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.216][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [636]. biodb.DEBUG[2024-07-06 16:04:18.217][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:18.217][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:18.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:18.222][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:18.223][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:18.224][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:18.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:18.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.233][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:18.233][private$selectFields] biodb.TRACE[2024-07-06 16:04:18.234][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:18.235][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:18.236][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:18.237][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.238][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.239][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.239][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.240][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.241][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.242][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.243][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.244][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:18.245][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:18.246][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.247][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.247][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.248][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.249][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:18.250][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.254][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.257][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.261][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [3014]. biodb.DEBUG[2024-07-06 16:04:18.262][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:18.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:18.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:18.267][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:18.268][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:18.269][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:18.270][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:18.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.278][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:18.279][private$selectFields] biodb.TRACE[2024-07-06 16:04:18.280][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:18.281][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:18.281][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:18.282][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.283][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.284][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.285][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.286][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.287][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.288][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.288][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.289][private$selectFields] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:18.290][private$organizeFieldsByGroups] Fields [1]: "chebi.id" biodb.TRACE[2024-07-06 16:04:18.291][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.292][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.293][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.294][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.294][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()" biodb.TRACE[2024-07-06 16:04:18.295][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.303][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.305][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.306][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [7799]. biodb.DEBUG[2024-07-06 16:04:18.307][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:18.308][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-07-06 16:04:18.323][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-07-06 16:04:18.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-07-06 16:04:18.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.327][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-07-06 16:04:18.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-07-06 16:04:18.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.330][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-07-06 16:04:18.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-07-06 16:04:18.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.333][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-07-06 16:04:18.336][biodb::testThat] biodb.INFO [2024-07-06 16:04:18.337][biodb::testThat] Running test function test_annotateMzValues_additional_fields (" Additional fields are accepted in annotateMzValues() "). biodb.INFO [2024-07-06 16:04:18.338][biodb::testThat] -------------------------------------------------------------------------------- biodb.INFO [2024-07-06 16:04:18.339][biodb::testThat] biodb.TRACE[2024-07-06 16:04:18.341][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-07-06 16:04:18.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-07-06 16:04:18.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.345][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-07-06 16:04:18.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-07-06 16:04:18.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.348][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.349][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass. biodb.TRACE[2024-07-06 16:04:18.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass. biodb.TRACE[2024-07-06 16:04:18.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.352][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.356][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.359][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.363][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.366][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.370][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.374][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.388][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:18.397][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:18.398][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:18.399][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:18.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:18.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:18.405][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:18.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:18.408][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:18.411][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:18.412][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-07-06 16:04:18.413][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:18.414][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-07-06 16:04:18.416][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:18.417][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:18.418][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:18.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:18.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:18.423][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:18.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:18.425][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.429][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:18.436][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:18.439][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:18.440][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-07-06 16:04:18.441][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:18.443][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-07-06 16:04:18.445][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:18.446][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:18.447][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:18.450][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:18.451][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:18.452][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:18.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:18.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:18.465][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:18.465][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:18.466][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:18.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:18.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:18.472][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:18.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:18.473][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.477][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.486][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:18.490][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:18.491][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:18.492][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:18.493][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:18.497][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:18.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:18.498][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:18.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:18.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:18.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:18.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:18.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:18.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.506][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.507][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:18.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:18.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.511][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:18.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:18.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.514][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.518][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.521][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:18.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:18.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.525][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:18.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:18.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.528][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:18.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:18.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.532][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:18.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:18.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.535][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:18.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:18.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.538][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:18.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:18.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.542][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:18.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:18.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.545][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.545][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:18.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:18.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.556][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.563][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:18.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:18.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.566][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:18.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:18.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.570][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:18.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:18.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.573][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:18.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:18.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.577][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:18.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:18.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.580][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:18.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:18.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.584][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:18.585][private$selectFields] biodb.TRACE[2024-07-06 16:04:18.586][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:18.587][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:18.587][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:18.588][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:18.589][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:18.590][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.591][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.592][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:18.593][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:18.594][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.594][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.595][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.596][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.597][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.598][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.599][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:18.600][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:18.601][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.602][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.602][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:18.603][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:18.604][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.605][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.606][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:18.607][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:18.608][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.609][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.609][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:18.610][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:18.611][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.612][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.613][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.614][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.615][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.616][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.616][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.617][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.618][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.619][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.620][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:18.621][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:18.622][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.623][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.624][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:18.625][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:18.625][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.626][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.627][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:18.628][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:18.629][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.630][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.631][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:18.632][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:18.632][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.633][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.634][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:18.635][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:18.636][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.637][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.638][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.639][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.639][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.640][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.641][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:18.642][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:18.643][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.644][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.645][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:18.646][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:18.647][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.647][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.648][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:18.649][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:18.650][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.651][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.652][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:18.653][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:18.654][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.654][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.655][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.656][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.657][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.658][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.659][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.660][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.661][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.661][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.662][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:18.663][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:18.664][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.665][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.666][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:18.667][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:18.668][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.668][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.669][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:18.670][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:18.671][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.672][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.673][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:18.674][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:18.675][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:18.676][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:18.677][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.677][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.678][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:18.679][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:18.680][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.681][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.682][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.683][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.684][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.684][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.685][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:18.686][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:18.687][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.688][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.689][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:18.690][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:18.691][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.691][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.692][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:18.693][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:18.694][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.695][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.696][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.697][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.698][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.698][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.699][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.700][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.701][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.702][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.703][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:18.704][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:18.705][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.705][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.706][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:18.707][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:18.708][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.709][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.710][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:18.711][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:18.712][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.712][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.713][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:18.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:18.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:18.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.718][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:18.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:18.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:18.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:18.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.725][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:18.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:18.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.728][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.729][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:18.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:18.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.732][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:18.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:18.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.735][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.739][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.740][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.743][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.747][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:18.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:18.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.750][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.750][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:18.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:18.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.754][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:18.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:18.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.758][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:18.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:18.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.766][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:18.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:18.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.770][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:18.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:18.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:18.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:18.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.777][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:18.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:18.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.781][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:18.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:18.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.783][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.784][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.790][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.791][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.797][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.802][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.804][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.805][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:18.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:18.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.809][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:18.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:18.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.812][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:18.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:18.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.816][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:18.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:18.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:18.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:18.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.823][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:18.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:18.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.827][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:18.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:18.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.830][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:18.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:18.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.834][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:18.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:18.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.844][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [192288, 0, 192288, C27H54O2, InChI=1S/C27H54O2/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-25-26-27(28)29-2/h3-26H2,1-2H3, ...]. biodb.DEBUG[2024-07-06 16:04:18.845][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:18.846][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:18.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:18.850][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:18.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:18.852][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:18.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:18.854][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:18.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:18.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:18.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:18.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.860][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.861][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:18.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:18.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.863][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.864][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:18.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:18.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.867][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.868][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.871][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.875][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:18.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:18.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.878][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.879][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:18.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:18.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.881][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.882][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:18.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:18.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.886][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:18.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:18.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.888][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.889][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:18.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:18.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.893][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:18.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:18.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.896][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:18.897][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:18.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.900][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:18.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:18.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.903][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.907][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.914][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.918][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:18.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:18.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.921][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:18.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:18.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.924][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.925][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:18.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:18.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.928][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:18.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:18.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.932][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:18.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:18.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.935][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:18.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:18.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.939][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:18.940][private$selectFields] biodb.TRACE[2024-07-06 16:04:18.941][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:18.942][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:18.942][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:18.943][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:18.944][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:18.945][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.946][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.947][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:18.948][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:18.949][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.949][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.950][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.951][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.952][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.953][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.954][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:18.955][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:18.956][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.956][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.957][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:18.958][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:18.959][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.960][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.961][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:18.962][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:18.963][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.964][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.964][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:18.965][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:18.966][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.967][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.968][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.969][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:18.970][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.971][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.972][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.973][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:18.973][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.974][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.975][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:18.976][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:18.977][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.978][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.979][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:18.980][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:18.980][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.981][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.982][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:18.983][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:18.984][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.985][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.986][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:18.987][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:18.987][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.988][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.989][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:18.990][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:18.991][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.992][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.993][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.994][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:18.994][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.995][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:18.996][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:18.997][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:18.998][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:18.999][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.000][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.001][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.001][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.002][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.003][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.004][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.005][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.006][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.007][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.008][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.008][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.009][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.010][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.011][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.012][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.013][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.014][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.015][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.016][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.016][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.017][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.018][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.019][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.020][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.021][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.022][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.023][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.023][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.024][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.025][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.026][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.027][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.028][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:19.029][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:19.030][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.031][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.031][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.032][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.033][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.034][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.035][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.036][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.037][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.038][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.044][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.045][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.045][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.046][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.047][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.048][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.049][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.050][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.051][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.052][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.053][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.053][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.054][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.055][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.056][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.057][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.058][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.059][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.059][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.060][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.061][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.062][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.063][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.064][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.065][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.066][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.066][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.067][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.068][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.069][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.070][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.071][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.072][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.072][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.073][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.074][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.075][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.076][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.077][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:19.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.085][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.088][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.092][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.095][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.099][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.106][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.110][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.113][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.117][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.119][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.120][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.124][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.127][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.131][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.135][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.138][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.142][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.145][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.149][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.152][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.153][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.156][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.159][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.164][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.167][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.170][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.174][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.178][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.182][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.185][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.192][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.195][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.196][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.199][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.200][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.203][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.206][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.212][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [15440, 0, 15440, C30H50, InChI=1S/C30H50/c1-25(2)15-11-19-29(7)23-13-21-27(5)17-9-10-18-28(6)22-14-24-30(8)20-12-16-26(3)4/h15-18,23-24H,9-14,19-22H2,1-8H3/b27-17+,28-18+,29-23+,30-24+, ...]. biodb.DEBUG[2024-07-06 16:04:19.213][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:19.214][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:19.215][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:19.219][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:19.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:19.220][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:19.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:19.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.229][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.233][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.236][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.239][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.240][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.244][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.247][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.251][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.254][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.258][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.261][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.265][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.268][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.272][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.275][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.278][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.279][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.283][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.286][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.290][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.293][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.297][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.299][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.300][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.304][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.307][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:19.308][private$selectFields] biodb.TRACE[2024-07-06 16:04:19.309][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:19.310][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:19.311][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:19.312][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.313][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.313][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.314][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.315][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.321][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.322][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.323][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.324][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.324][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.325][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.326][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.327][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.328][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.329][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.330][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.331][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.331][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.332][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.333][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.334][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.335][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.336][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.337][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.337][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.338][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.339][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.340][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.341][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.342][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.343][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.344][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.344][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.345][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.346][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.347][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.348][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.349][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.350][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.350][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.351][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.352][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.353][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.354][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.355][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.356][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.357][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.357][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.358][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.359][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.360][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.361][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.362][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.363][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.363][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.364][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.365][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.366][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.367][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.368][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.369][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.370][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.370][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.371][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.372][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.373][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.374][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.375][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.376][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.376][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.377][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.378][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.379][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.380][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.381][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.382][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.382][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.383][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.384][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.385][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.386][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.387][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.388][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.388][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.389][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.390][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.391][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.392][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.393][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.394][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.395][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.395][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.396][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.397][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.398][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.399][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.400][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:19.401][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:19.401][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.402][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.403][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.404][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.405][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.406][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.407][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.407][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.408][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.409][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.410][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.411][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.412][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.413][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.414][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.414][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.415][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.416][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.417][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.418][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.419][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.420][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.421][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.421][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.422][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.423][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.424][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.425][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.426][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.427][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.428][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.428][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.429][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.430][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.431][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.432][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.433][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.434][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.435][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.435][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.436][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.437][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.438][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.439][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.440][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:19.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.444][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.444][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.451][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.452][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.455][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.459][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.463][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.473][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.477][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.480][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.484][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.488][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.491][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.494][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.495][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.498][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.501][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.502][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.505][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.513][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.516][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.523][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.527][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.531][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.534][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.538][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.541][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.542][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.545][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.549][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.552][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.556][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.564][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [209892, 0, 209892, C30H50, InChI=1S/C30H50/c1-21(2)11-9-12-22(3)23-15-19-30(8)25-13-14-26-27(4,5)17-10-18-28(26,6)24(25)16-20-29(23,30)7/h11,13,22-24,26H,9-10,12,14-20H2,1-8H3/t22-,23+,24+,26+,28-,29+,30-/m1/s1, ...]. biodb.DEBUG[2024-07-06 16:04:19.565][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:19.566][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:19.569][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:19.570][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:19.570][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:19.574][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:19.575][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:19.576][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:19.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:19.579][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:19.582][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:19.583][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b3cd8ddf08f509014f10dc9bf7c1649d". biodb.TRACE[2024-07-06 16:04:19.584][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:19.586][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b3cd8ddf08f509014f10dc9bf7c1649d.content". biodb.DEBUG[2024-07-06 16:04:19.588][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:19.588][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:19.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:19.598][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:19.599][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:19.600][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:19.601][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:19.602][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.609][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.611][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:19.612][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:19.613][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:19.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:19.618][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:19.619][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:19.619][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:19.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:19.621][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.625][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.628][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:19.633][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:19.635][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:19.637][cch$loadFileContent] Trying to load 1 files from cache: [1]: "831507e33c6cf42061851262412f5feb". biodb.TRACE[2024-07-06 16:04:19.638][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:19.639][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/831507e33c6cf42061851262412f5feb.content". biodb.DEBUG[2024-07-06 16:04:19.641][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:19.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:19.643][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:19.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:19.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:19.648][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:19.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:19.650][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.653][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.656][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.660][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:19.661][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:19.661][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:19.662][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:19.666][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:19.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:19.668][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:19.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:19.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.672][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.673][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.679][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:19.680][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:19.681][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:19.682][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:19.686][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:19.687][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:19.687][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:19.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:19.689][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.692][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.693][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.695][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:19.700][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:19.701][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:19.702][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:19.703][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:19.707][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:19.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:19.708][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:19.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:19.710][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.718][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.721][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.725][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.732][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.735][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.739][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.743][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.746][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.750][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.753][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.757][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.760][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.764][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.767][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.771][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.775][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.778][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.782][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.785][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.789][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.792][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.796][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:19.797][private$selectFields] biodb.TRACE[2024-07-06 16:04:19.798][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:19.798][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:19.799][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:19.800][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.801][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.802][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.803][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.804][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.805][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.806][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.806][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.807][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.808][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.809][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.810][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.811][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.812][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.813][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.813][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.814][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.815][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.816][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.817][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.818][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.819][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.820][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.820][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.821][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.822][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.823][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.824][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.825][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.826][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.827][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.827][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.828][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.829][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.830][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.831][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.832][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.833][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.834][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.834][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.835][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.836][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.837][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.838][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.839][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.840][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.841][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.841][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.842][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.843][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.844][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.845][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.846][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.847][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.848][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.848][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.849][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.850][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.851][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.852][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.853][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.854][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.855][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.855][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.856][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.857][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.858][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.859][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.860][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.861][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.862][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.863][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.863][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.864][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.865][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.866][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.867][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.868][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.869][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.870][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.870][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.871][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.877][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.878][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.879][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.880][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.881][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.882][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.883][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.884][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.885][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.885][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.886][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.887][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.888][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.889][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.890][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:19.891][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:19.891][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.892][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.893][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.894][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.895][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.896][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.897][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.898][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.898][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.899][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.900][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.901][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.902][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.903][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.904][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.904][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.905][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.906][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.907][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.908][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.909][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.910][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.910][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.911][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.912][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.913][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.914][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.915][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.916][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.917][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:19.917][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.918][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.919][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.920][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:19.921][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.922][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.922][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:19.923][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:19.924][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.925][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.926][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:19.927][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:19.928][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.928][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.929][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:19.930][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:19.931][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.932][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.933][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:19.934][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.941][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:19.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:19.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.944][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.948][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.951][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:19.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:19.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.955][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.959][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:19.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.966][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.970][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.973][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:19.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:19.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.977][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.979][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.980][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.984][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:19.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:19.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.988][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.991][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.995][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:19.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:19.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:19.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:19.998][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:19.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.002][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.006][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.009][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.013][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.020][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.031][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.034][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.038][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.042][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.045][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.049][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.051][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.052][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.056][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.059][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.068][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [4781, 0, 4781, C29H40N2O4, InChI=1S/C29H40N2O4/c1-6-18-17-31-10-8-20-14-27(33-3)29(35-5)16-23(20)25(31)12-21(18)11-24-22-15-28(34-4)26(32-2)13-19(22)7-9-30-24/h13-16,18,21,24-25,30H,6-12,17H2,1-5H3/t18-,21-,24+,25-/m0/s1, ...]. biodb.DEBUG[2024-07-06 16:04:20.069][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:20.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:20.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:20.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:20.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:20.077][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:20.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:20.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:20.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:20.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.082][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:20.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:20.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.086][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:20.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:20.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.089][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:20.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:20.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.092][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.093][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.096][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.100][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:20.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:20.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.103][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:20.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:20.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.107][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:20.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:20.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.110][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:20.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:20.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.114][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:20.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:20.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.117][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:20.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:20.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.121][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.124][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.128][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.135][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.138][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.142][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.145][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.146][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.154][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.158][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.162][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.165][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.169][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:20.170][private$selectFields] biodb.TRACE[2024-07-06 16:04:20.170][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:20.171][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:20.172][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:20.173][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:20.174][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:20.175][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.176][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.176][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:20.177][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:20.178][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.179][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.180][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.181][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.182][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.182][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.183][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:20.184][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:20.185][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.186][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.187][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:20.188][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:20.189][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.189][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.190][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:20.191][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:20.192][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.193][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.194][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.195][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.195][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.196][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.197][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.198][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.199][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.200][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.201][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.202][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.202][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.203][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.204][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.205][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.206][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.207][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.208][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.208][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.209][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.210][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.211][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.212][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.213][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.214][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.214][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:20.215][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:20.216][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.217][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.218][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:20.219][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:20.220][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.220][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.221][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.222][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.223][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.224][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.225][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:20.226][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:20.227][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.227][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.228][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:20.229][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:20.230][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.231][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.232][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:20.233][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:20.233][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.234][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.235][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.236][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.237][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.238][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.239][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.240][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.240][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.241][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.242][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.243][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.244][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.245][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.246][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.246][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.247][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.248][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.249][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.250][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.251][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.252][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.253][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.254][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.254][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.255][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.256][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:20.257][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:20.258][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:20.259][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:20.260][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.261][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.262][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:20.262][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:20.263][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.264][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.265][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.266][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.267][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.268][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.269][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:20.270][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:20.270][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.271][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.272][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:20.273][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:20.274][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.275][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.276][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:20.277][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:20.277][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.278][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.279][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.280][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.281][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.282][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.283][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.284][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.285][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.285][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.286][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.287][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.288][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.289][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.290][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.291][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.292][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.292][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.293][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.294][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.295][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.296][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.297][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.298][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.299][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.299][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.300][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:20.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:20.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:20.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:20.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:20.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:20.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:20.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.312][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:20.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:20.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.316][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:20.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:20.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.319][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:20.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:20.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.323][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.333][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.334][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:20.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:20.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.336][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.337][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:20.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:20.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.340][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.341][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:20.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:20.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.344][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.345][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:20.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:20.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.347][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.348][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:20.349][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:20.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.352][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:20.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:20.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.355][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:20.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:20.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.359][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:20.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:20.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.362][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:20.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:20.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.366][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.370][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.373][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.384][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.391][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.395][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.398][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.401][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.402][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.405][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.409][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.412][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.413][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.416][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.420][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.423][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.423][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.432][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.441][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [16587, 0, 16587, C27H44O7, InChI=1S/C27H44O7/c1-23(2,32)9-8-22(31)26(5,33)21-7-11-27(34)16-12-18(28)17-13-19(29)20(30)14-24(17,3)15(16)6-10-25(21,27)4/h12,15,17,19-22,29-34H,6-11,13-14H2,1-5H3/t15-,17-,19+,20-,21-,22+,24+,25+,26+,27+/m0/s1, ...]. biodb.DEBUG[2024-07-06 16:04:20.442][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:20.442][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:20.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:20.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:20.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:20.449][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:20.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:20.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:20.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:20.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.454][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:20.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:20.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.457][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.458][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:20.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:20.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.461][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:20.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:20.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.465][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.468][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.472][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:20.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:20.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.475][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:20.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:20.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.478][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:20.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:20.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.481][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.482][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:20.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:20.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:20.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:20.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.488][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.489][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:20.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:20.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.492][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.496][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.499][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.502][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.506][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.506][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.510][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.513][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.517][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.520][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.524][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.527][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.531][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.534][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.535][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:20.535][private$selectFields] biodb.TRACE[2024-07-06 16:04:20.536][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:20.537][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:20.538][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:20.539][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:20.540][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:20.541][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.542][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.542][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:20.543][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:20.544][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.545][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.546][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.547][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.548][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.549][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.549][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:20.550][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:20.551][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.552][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.553][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:20.554][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:20.555][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.556][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.557][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:20.557][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:20.558][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.559][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.560][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.561][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.562][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.563][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.564][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.565][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.565][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.566][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.567][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.568][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.569][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.570][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.571][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.572][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.572][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.573][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.574][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.575][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.576][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.577][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.578][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.579][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.579][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.580][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.581][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:20.582][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:20.583][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.584][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.585][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:20.586][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:20.586][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.587][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.588][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.589][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.590][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.591][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.592][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:20.593][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:20.593][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.594][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.595][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:20.596][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:20.597][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.598][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.599][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:20.600][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:20.600][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.601][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.602][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.603][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:20.604][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.605][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.606][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.607][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.608][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.608][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.609][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.610][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.611][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.612][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.613][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.614][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.615][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.615][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.616][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.617][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.618][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.619][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.620][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.621][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.622][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.622][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.623][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:20.624][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:20.625][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:20.626][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:20.627][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.628][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.629][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:20.630][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:20.630][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.631][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.632][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.633][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.634][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.635][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.636][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:20.636][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:20.637][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.638][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.639][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:20.640][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:20.641][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.642][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.643][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:20.643][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:20.644][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.645][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.646][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.647][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.648][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.649][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.650][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.650][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.651][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.652][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.653][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.654][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.655][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.656][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.656][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.657][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.658][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.659][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.660][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.661][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.662][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.663][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.664][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:20.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:20.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:20.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:20.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:20.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.671][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:20.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:20.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.674][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.675][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:20.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:20.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.679][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:20.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:20.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.681][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.682][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:20.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:20.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.685][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.686][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.689][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.690][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.692][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.693][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:20.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.697][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:20.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:20.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.705][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:20.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:20.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.708][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.709][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:20.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:20.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.713][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:20.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:20.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.715][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.716][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:20.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:20.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.720][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:20.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:20.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.723][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:20.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:20.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.727][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:20.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:20.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.729][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.730][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:20.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:20.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.734][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.737][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.740][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.744][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.748][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.751][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.751][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:20.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.754][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.755][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.758][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.758][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.761][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.762][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:20.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:20.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.769][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.773][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:20.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:20.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.776][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.779][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.780][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.783][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:20.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:20.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.786][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.791][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [19804, 0, 19804, C27H44O7, InChI=1S/C27H44O7/c1-23(2,32)8-5-9-26(33,15-28)22-7-11-27(34)17-12-19(29)18-13-20(30)21(31)14-24(18,3)16(17)6-10-25(22,27)4/h12,16,18,20-22,28,30-34H,5-11,13-15H2,1-4H3/t16-,18-,20+,21-,22-,24+,25+,26+,27+/m0/s1, ...]. biodb.DEBUG[2024-07-06 16:04:20.792][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:20.793][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:20.796][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:20.796][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:20.797][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:20.801][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:20.802][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:20.803][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:20.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:20.806][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:20.809][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:20.810][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26d0872875c47c33e8205aa7124e0486". biodb.TRACE[2024-07-06 16:04:20.811][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:20.812][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26d0872875c47c33e8205aa7124e0486.content". biodb.DEBUG[2024-07-06 16:04:20.815][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:20.815][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:20.816][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:20.820][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:20.821][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:20.822][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:20.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:20.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.827][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.833][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:20.834][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:20.835][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:20.836][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:20.840][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:20.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:20.841][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:20.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:20.843][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.847][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.850][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:20.854][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:20.855][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:20.856][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:20.859][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:20.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:20.861][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:20.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:20.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.867][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.870][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:20.874][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:20.875][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:20.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:20.879][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:20.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:20.881][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:20.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:20.883][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.886][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.890][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:20.893][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:20.894][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:20.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:20.899][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:20.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:20.900][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:20.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:20.902][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.906][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.908][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.909][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:20.913][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:20.914][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:20.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:20.918][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:20.919][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:20.920][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:20.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:20.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.924][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.929][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:20.932][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:20.933][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:20.934][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:20.938][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:20.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:20.940][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:20.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:20.941][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.945][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.949][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:20.952][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:20.953][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:20.954][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:20.958][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:20.958][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:20.959][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:20.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:20.961][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.965][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:20.972][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:20.975][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:20.976][cch$loadFileContent] Trying to load 1 files from cache: [1]: "357534c211a0779cb44e196fcebae6c0". biodb.TRACE[2024-07-06 16:04:20.978][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:20.984][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/357534c211a0779cb44e196fcebae6c0.content". biodb.DEBUG[2024-07-06 16:04:20.986][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:20.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:20.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:20.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:20.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:20.993][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:20.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:20.995][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:20.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:20.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:20.999][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.002][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:21.006][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:21.007][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:21.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:21.011][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:21.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:21.013][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:21.013][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:21.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.017][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.018][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.022][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.024][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:21.025][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:21.026][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:21.027][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:21.031][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:21.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:21.032][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:21.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:21.034][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.041][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:21.045][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:21.046][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:21.047][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:21.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:21.051][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:21.052][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:21.053][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:21.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:21.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.058][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.062][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.065][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.072][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.076][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.078][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.079][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.083][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.085][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.086][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.090][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.093][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.094][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.096][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.097][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.101][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.104][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.111][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.115][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.118][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.122][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.126][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.129][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.133][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.136][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.140][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:21.141][private$selectFields] biodb.TRACE[2024-07-06 16:04:21.141][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:21.142][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:21.143][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:21.144][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.145][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.146][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.147][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.148][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.149][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.149][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.150][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.151][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.152][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.153][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.154][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.155][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.156][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.157][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.157][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.158][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.159][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.160][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.161][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.162][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.163][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.164][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.164][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.165][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.166][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.167][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.168][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.169][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.170][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.171][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.171][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.172][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.173][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.174][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.175][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.176][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.177][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.178][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.178][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.179][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.180][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.181][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.182][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.183][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.184][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.185][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.185][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.186][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.187][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.188][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.189][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.190][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.191][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.192][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.192][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.193][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.194][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.195][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.196][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.197][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.198][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.199][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.200][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.200][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.201][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.202][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.203][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.204][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.205][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.206][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.207][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.207][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.208][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.209][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.210][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.211][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.212][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.213][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.214][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.215][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.215][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.216][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.217][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.218][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.219][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.220][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.221][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.222][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.223][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.223][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.224][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.225][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.226][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.227][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.228][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.229][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:21.230][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:21.230][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.231][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.232][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.233][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.234][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.235][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.236][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.237][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.238][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.238][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.239][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.240][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.241][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.242][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.243][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.244][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.245][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.246][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.246][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.247][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.248][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.249][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.250][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.251][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.252][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.253][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.253][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.254][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.260][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.261][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.262][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.263][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.264][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.265][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.266][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.267][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.268][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.269][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.270][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.270][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.271][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.272][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.273][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.274][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.275][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.276][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.276][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.277][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.278][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:21.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.286][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.290][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.293][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.296][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.297][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.300][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.311][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.315][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.318][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.322][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.325][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.329][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.332][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.336][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.339][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.343][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.347][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.350][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.353][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.356][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.357][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.360][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.361][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.364][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.367][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.371][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.372][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.375][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.378][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.379][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.382][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.386][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.389][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.390][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.393][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.397][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.400][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.400][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.404][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.407][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.413][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [7799, 0, 7799, C16H31N2O8P, InChI=1S/C16H28N2O4.H3O4P/c1-5-12(6-2)22-14-9-11(16(20)21-7-3)8-13(17)15(14)18-10(4)19;1-5(2,3)4/h9,12-15H,5-8,17H2,1-4H3,(H,18,19);(H3,1,2,3,4)/t13-,14+,15+;/m0./s1, ...]. biodb.DEBUG[2024-07-06 16:04:21.414][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:21.415][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:21.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:21.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:21.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:21.421][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:21.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:21.423][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.427][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.430][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.434][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.436][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.441][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.444][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.448][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.451][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.454][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.455][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.458][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.461][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.462][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.465][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.465][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.468][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.469][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.473][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.475][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.476][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.479][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.486][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.487][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.490][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.494][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.497][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.501][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.504][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.508][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:21.509][private$selectFields] biodb.TRACE[2024-07-06 16:04:21.510][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:21.511][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:21.511][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:21.512][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.513][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.514][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.515][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.516][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.517][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.518][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.518][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.519][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.520][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.521][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.522][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.523][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.524][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.525][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.525][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.526][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.527][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.528][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.529][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.530][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.531][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.536][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.537][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.538][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.539][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.540][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.541][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.542][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.543][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.544][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.545][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.545][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.546][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.547][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.548][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.549][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.550][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.551][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.551][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.552][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.553][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.554][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.555][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.556][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.557][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.558][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.558][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.559][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.560][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.561][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.562][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.563][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.564][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.564][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.565][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.566][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.567][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.568][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.569][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.570][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.570][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.571][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.572][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.573][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.574][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.575][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.576][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.576][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.577][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.578][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.579][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.580][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.581][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.582][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.583][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.583][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.584][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.585][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.586][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.587][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.588][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.589][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.589][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.590][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.591][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.592][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.593][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.594][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.595][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.595][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.596][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.597][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.598][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.599][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.600][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.601][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:21.601][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:21.602][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.603][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.604][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.605][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.606][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.607][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.608][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.608][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.609][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.610][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.611][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.612][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.613][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.614][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.614][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.615][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.616][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.617][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.618][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.619][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.619][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.620][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.621][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.622][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.623][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.624][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.625][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.626][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.626][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.627][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.628][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.629][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.630][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.631][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.632][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.632][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.633][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.634][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.635][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.636][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.637][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.638][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.639][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.639][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.640][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:21.641][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.652][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.655][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.656][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.659][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.663][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.667][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.674][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.677][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.681][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.685][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.688][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.692][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.695][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.699][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.702][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.705][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.706][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.709][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.709][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.712][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.713][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.716][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.727][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.730][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.731][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.734][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.738][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.742][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.745][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.748][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.749][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.752][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.756][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.765][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [71954, 0, 71954, C18H21F3N6O2, InChI=1S/C18H21F3N6O2/c19-18(20,21)13-9-15(22)23-11-12(13)14-10-16(26-1-5-28-6-2-26)25-17(24-14)27-3-7-29-8-4-27/h9-11H,1-8H2,(H2,22,23), ...]. biodb.DEBUG[2024-07-06 16:04:21.766][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:21.767][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:21.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:21.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:21.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:21.773][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:21.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:21.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.779][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.782][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.786][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.789][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.793][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.796][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.800][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.803][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.811][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.812][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.815][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.816][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.819][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.822][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.823][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.826][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.829][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.830][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.833][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.837][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.844][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.847][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.851][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.854][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.858][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.860][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.861][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.865][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:21.865][private$selectFields] biodb.TRACE[2024-07-06 16:04:21.866][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:21.867][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:21.868][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:21.869][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.870][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.871][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.871][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.872][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.873][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.874][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.875][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.876][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.877][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.877][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.878][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.879][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.880][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.881][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.882][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.882][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.883][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.884][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.885][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.886][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.887][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.888][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.889][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.889][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.890][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.891][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.892][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.893][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.894][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.895][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.895][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.896][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.897][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.898][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.899][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.900][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.901][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.902][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.902][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.903][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.904][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.905][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.906][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.907][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.908][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.909][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.909][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.910][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.911][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.912][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.913][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.914][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.915][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.916][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.916][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.917][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.918][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.919][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.920][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.921][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.922][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.923][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.923][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.924][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.925][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.926][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.927][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.928][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.929][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.930][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.930][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.931][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.932][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:21.933][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.934][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.935][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.936][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.937][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.938][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.938][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.939][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.940][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.941][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.942][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.943][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.944][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.945][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.945][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.946][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.947][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.948][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.949][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.950][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.951][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.952][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.952][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:21.953][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:21.954][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.955][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.956][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.957][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.958][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:21.959][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:21.960][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.960][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.961][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.962][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:21.963][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.964][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.965][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:21.966][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:21.967][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.967][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.968][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:21.969][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:21.970][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.971][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.972][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:21.973][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:21.974][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.974][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.975][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.976][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:21.977][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.978][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.979][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.980][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:21.981][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.981][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.982][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:21.983][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:21.984][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.985][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.986][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:21.987][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:21.988][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.989][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.989][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:21.990][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:21.991][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.992][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.993][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:21.994][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:21.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:21.997][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:21.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:21.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.005][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.008][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.012][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.016][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.019][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.026][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.030][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.033][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.036][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.037][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.041][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.044][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.048][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.051][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.058][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.065][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.066][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.072][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.073][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.076][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.076][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.079][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.080][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.089][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.092][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.096][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.099][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.100][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.103][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.107][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.110][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.114][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.122][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [197612, 0, 197612, C18H18O9S, InChI=1S/C18H18O9S/c1-7-3-9(19)13-11(4-7)27-16-8(14(13)21)5-12(28-16)18(25,17(24)26-2)6-10(20)15(22)23/h3-4,10,12,19-20,25H,5-6H2,1-2H3,(H,22,23)/t10-,12+,18?/m1/s1, ...]. biodb.DEBUG[2024-07-06 16:04:22.123][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:22.123][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:22.131][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:22.131][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:22.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:22.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:22.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:22.138][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:22.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:22.141][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:22.144][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:22.145][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1". biodb.TRACE[2024-07-06 16:04:22.146][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:22.147][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content". biodb.DEBUG[2024-07-06 16:04:22.149][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:22.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:22.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:22.155][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:22.155][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:22.156][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:22.157][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:22.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.161][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:22.169][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:22.172][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:22.173][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6". biodb.TRACE[2024-07-06 16:04:22.174][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:22.175][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content". biodb.DEBUG[2024-07-06 16:04:22.177][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:22.178][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:22.179][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:22.183][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:22.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:22.184][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:22.185][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:22.186][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.190][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.192][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.196][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:22.197][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:22.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:22.198][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:22.202][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:22.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:22.204][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:22.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:22.206][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.209][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.213][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:22.217][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:22.218][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:22.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:22.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:22.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:22.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:22.225][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:22.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:22.227][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.234][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.238][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.241][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.248][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.252][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.254][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.255][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.259][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.266][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.269][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.270][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.273][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.276][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.277][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.287][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.291][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.293][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.294][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.297][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.298][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.301][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.305][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.308][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.312][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:22.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:22.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.316][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:22.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:22.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.319][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:22.320][private$selectFields] biodb.TRACE[2024-07-06 16:04:22.321][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:22.322][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:22.322][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:22.323][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.324][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.325][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.326][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.327][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.328][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.329][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.330][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.330][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.331][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.332][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.333][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.334][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.335][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.336][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.337][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.337][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.338][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.339][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.340][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.341][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.342][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.343][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.344][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.344][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.345][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.346][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.347][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.348][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.349][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.350][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.351][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.351][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.352][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.353][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.354][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.355][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.356][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.357][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.366][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.367][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.368][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.369][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.370][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.371][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.372][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.373][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.374][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.375][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:22.376][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:22.377][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.377][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.378][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.379][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.380][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.381][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.382][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.383][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.383][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.384][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.385][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.386][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.387][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.388][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.389][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.389][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.390][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.391][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.392][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.393][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.394][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.395][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.395][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.396][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.397][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.398][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.399][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.400][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.401][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.401][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.402][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.403][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.404][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.405][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.406][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.407][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.408][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.408][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.409][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.410][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.411][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.412][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.413][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.414][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.414][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.415][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.416][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.417][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.418][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.419][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.420][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:22.421][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:22.421][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.422][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.423][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:22.424][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:22.425][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.426][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.427][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.427][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.428][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.429][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.430][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.431][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.432][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.433][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.433][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.434][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.435][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.436][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.437][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.438][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.439][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.439][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.440][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.441][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.442][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.443][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.444][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.445][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.445][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.446][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.447][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.448][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.449][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.450][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.451][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.451][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.452][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.453][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.454][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.455][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.456][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.457][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.458][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.458][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.459][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.460][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.461][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.462][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.463][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:22.464][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.466][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.475][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.477][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.478][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.481][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.482][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.488][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.489][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.495][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.496][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.499][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.500][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.503][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.504][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.506][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.507][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.511][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.514][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.517][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.518][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.522][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.525][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.528][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.540][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.550][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.551][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.554][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.557][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.558][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.562][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.564][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.565][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.569][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.572][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.576][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.578][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.579][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.582][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.588][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [192288, 0, 192288, C27H54O2, InChI=1S/C27H54O2/c1-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-20-21-22-23-24-25-26-27(28)29-2/h3-26H2,1-2H3, ...]. biodb.DEBUG[2024-07-06 16:04:22.589][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:22.590][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:22.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:22.594][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:22.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:22.596][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:22.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:22.598][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.602][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.605][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.609][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.611][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.616][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.618][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.619][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.623][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.625][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.626][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.629][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.630][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.633][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.636][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.637][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.645][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.646][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.649][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.649][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.653][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.656][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.657][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.659][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.663][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.664][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.667][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.671][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.674][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.678][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.681][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.685][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.688][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:22.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:22.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.691][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.691][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:22.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:22.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.695][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:22.696][private$selectFields] biodb.TRACE[2024-07-06 16:04:22.697][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:22.697][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:22.698][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:22.699][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.700][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.701][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.702][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.703][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.704][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.704][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.705][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.706][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.707][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.708][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.709][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.710][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.710][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.711][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.712][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.713][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.714][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.715][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.716][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.716][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.717][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.718][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.719][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.720][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.721][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.722][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.722][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.723][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.724][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.725][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.726][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.727][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.728][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.729][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.729][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.730][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.731][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.732][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.733][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.734][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.735][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.735][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.736][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.737][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.738][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.739][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.740][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.741][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:22.742][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:22.742][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.743][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.744][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.745][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.746][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.747][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.748][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.749][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.749][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.750][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.751][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.752][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.753][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.754][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.755][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.756][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.757][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.757][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.758][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.759][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.760][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.761][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.762][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.763][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.764][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.764][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.765][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.766][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.767][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.768][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.769][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.770][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.771][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.771][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.772][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.773][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.774][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.775][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.776][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.777][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.778][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.778][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.779][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.780][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.781][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.782][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.783][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.784][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.785][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.785][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.786][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:22.787][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:22.788][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.789][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.790][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:22.791][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:22.792][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.793][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.793][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.794][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.795][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.796][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.797][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.798][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.799][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.800][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.800][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.801][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.802][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.803][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.804][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.805][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.806][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.807][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.807][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.808][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.809][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.810][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.811][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.812][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.813][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.814][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.814][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.815][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.816][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.817][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.818][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.819][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.820][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.821][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.821][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.822][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.823][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.824][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.825][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.826][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.827][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.828][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.828][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.829][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.830][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.831][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.832][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.833][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.834][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:22.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.838][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.845][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.849][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.852][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.860][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.863][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.867][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.870][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.870][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.873][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.874][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:22.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:22.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.877][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.878][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.881][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.884][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.885][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:22.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:22.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.888][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.892][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.895][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.895][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:22.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:22.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.899][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.902][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.903][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.906][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:22.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.909][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.910][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.913][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.922][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:22.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.926][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.930][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.932][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.933][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:22.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.937][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.940][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.944][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:22.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:22.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.948][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.954][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:22.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:22.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.958][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.962][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.965][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:22.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:22.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.974][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [15440, 0, 15440, C30H50, InChI=1S/C30H50/c1-25(2)15-11-19-29(7)23-13-21-27(5)17-9-10-18-28(6)22-14-24-30(8)20-12-16-26(3)4/h15-18,23-24H,9-14,19-22H2,1-8H3/b27-17+,28-18+,29-23+,30-24+, ...]. biodb.DEBUG[2024-07-06 16:04:22.975][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:22.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:22.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:22.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:22.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:22.982][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:22.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:22.984][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.986][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.987][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:22.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:22.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.991][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.993][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.994][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:22.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:22.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:22.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:22.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:22.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.005][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.008][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.012][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.015][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.019][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.022][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.026][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.029][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.033][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.036][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.037][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.040][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.044][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.046][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.047][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.051][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.053][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.054][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.058][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.061][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.061][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.064][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.065][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.068][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.069][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.071][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.072][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.075][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.076][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:23.076][private$selectFields] biodb.TRACE[2024-07-06 16:04:23.077][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:23.078][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:23.079][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:23.080][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:23.081][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:23.082][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.083][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.083][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:23.084][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:23.085][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.086][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.087][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.088][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.089][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.090][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.090][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.091][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.092][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.093][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.094][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.095][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.096][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.097][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.097][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.098][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.099][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.100][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.101][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.102][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.103][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.104][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.104][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.105][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.106][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.107][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.108][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.109][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.110][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.111][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.111][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.112][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.113][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.114][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.115][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.116][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.117][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.118][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.118][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.119][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.120][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.121][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.122][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.123][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.124][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.125][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.125][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:23.126][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:23.127][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.128][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.129][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:23.130][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:23.131][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.132][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.132][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.133][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.134][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.135][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.136][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.137][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.138][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.139][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.139][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.140][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.141][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.142][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.143][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.144][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.145][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.146][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.146][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.147][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.148][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.149][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.150][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.151][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.152][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.153][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.153][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.154][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.155][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.156][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.157][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.158][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.159][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.160][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.160][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.161][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.162][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.163][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.164][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.165][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.166][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.167][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.167][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.168][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.169][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.170][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.171][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:23.172][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:23.173][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:23.174][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:23.175][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.175][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.176][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:23.177][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:23.178][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.179][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.180][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.181][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.182][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.182][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.183][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.184][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.185][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.186][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.187][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.188][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.189][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.189][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.190][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.191][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.197][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.198][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.199][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.200][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.201][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.202][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.203][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.204][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.205][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.206][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.206][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.207][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.208][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.209][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.210][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.211][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.212][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.213][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.213][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.214][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.215][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.216][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.217][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:23.218][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:23.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:23.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.220][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:23.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:23.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.224][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:23.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:23.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.228][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:23.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:23.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.231][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.232][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:23.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:23.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.235][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:23.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:23.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.238][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.239][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.243][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.246][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.249][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.250][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.253][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.256][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.257][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.260][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.264][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.267][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.271][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.274][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.278][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.282][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.285][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.289][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.292][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.299][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.303][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.307][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.309][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.310][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.314][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.317][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.321][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.325][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.327][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.328][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.332][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.334][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.340][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [209892, 0, 209892, C30H50, InChI=1S/C30H50/c1-21(2)11-9-12-22(3)23-15-19-30(8)25-13-14-26-27(4,5)17-10-18-28(26,6)24(25)16-20-29(23,30)7/h11,13,22-24,26H,9-10,12,14-20H2,1-8H3/t22-,23+,24+,26+,28-,29+,30-/m1/s1, ...]. biodb.DEBUG[2024-07-06 16:04:23.341][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:23.342][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:23.345][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:23.345][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:23.346][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:23.350][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:23.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:23.352][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:23.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:23.355][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.62*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:23.358][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:23.359][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b3cd8ddf08f509014f10dc9bf7c1649d". biodb.TRACE[2024-07-06 16:04:23.360][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:23.362][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b3cd8ddf08f509014f10dc9bf7c1649d.content". biodb.DEBUG[2024-07-06 16:04:23.364][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:23.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:23.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:23.369][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:23.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:23.371][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:23.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:23.372][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.376][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.382][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:23.383][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:23.384][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:23.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:23.389][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:23.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:23.390][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:23.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:23.392][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:23.403][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.63*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:23.406][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:23.407][cch$loadFileContent] Trying to load 1 files from cache: [1]: "831507e33c6cf42061851262412f5feb". biodb.TRACE[2024-07-06 16:04:23.409][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:23.410][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/831507e33c6cf42061851262412f5feb.content". biodb.DEBUG[2024-07-06 16:04:23.412][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:23.413][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:23.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:23.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:23.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:23.419][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:23.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:23.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.425][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.427][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.428][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:23.432][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:23.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:23.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:23.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:23.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:23.439][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:23.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:23.441][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.444][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.448][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:23.451][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:23.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:23.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:23.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:23.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:23.458][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:23.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:23.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.463][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.464][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.465][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.466][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.470][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:23.476][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:23.478][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:23.479][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:23.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:23.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:23.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:23.485][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:23.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:23.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:23.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:23.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.491][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:23.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:23.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.494][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:23.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:23.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.498][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:23.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:23.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.508][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.511][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.512][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.515][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.519][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.522][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.526][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.528][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.529][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.533][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.536][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.540][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.543][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.547][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.550][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.554][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.557][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.561][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.564][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.568][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.571][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.575][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.578][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:23.579][private$selectFields] biodb.TRACE[2024-07-06 16:04:23.580][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:23.581][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:23.582][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:23.583][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:23.583][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:23.584][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.585][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.586][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:23.587][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:23.588][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.589][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.590][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.591][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.591][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.592][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.593][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.594][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.595][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.596][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.597][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.598][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.599][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.599][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.600][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.601][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.602][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.603][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.604][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.605][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.606][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.606][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.607][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.608][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.609][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.610][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.611][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.612][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.613][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.614][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.614][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.615][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.616][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.617][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.618][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.619][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.620][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.621][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.621][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.622][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.623][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.624][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.625][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.626][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.627][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.628][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.628][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:23.629][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:23.630][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.631][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.632][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:23.633][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:23.634][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.635][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.635][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.636][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.637][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.638][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.639][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.640][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.641][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.642][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.643][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.643][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.644][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.645][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.646][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.647][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.648][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.649][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.650][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.651][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.651][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.652][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.653][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.654][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.655][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.656][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.657][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.658][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.658][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.659][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.660][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.661][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.662][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.663][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.664][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.665][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.666][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.666][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.667][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.668][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.669][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.670][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.671][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.672][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.673][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.673][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.674][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:23.675][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:23.676][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:23.677][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:23.678][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.679][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.680][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:23.681][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:23.681][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.682][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.683][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.684][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.685][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.686][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.687][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.688][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.688][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.689][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.690][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.691][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.692][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.693][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.694][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.695][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.695][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.696][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.697][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.698][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.699][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.700][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.701][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.702][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.702][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.703][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.704][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.705][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.706][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.707][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.708][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.709][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.709][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.710][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.711][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.712][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.713][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.714][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.715][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.716][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.716][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.717][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.718][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:23.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:23.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:23.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.722][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.723][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:23.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:23.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.725][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:23.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:23.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.729][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.730][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:23.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:23.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.733][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:23.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:23.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.737][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:23.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:23.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.740][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.741][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.743][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.744][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.747][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.748][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.757][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.761][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.764][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.768][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.771][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.775][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.779][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.782][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.786][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.788][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.789][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.793][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.796][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.800][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.803][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.806][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.807][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.810][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.814][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.815][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.820][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.821][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.824][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.828][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.832][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.835][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.839][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.842][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.846][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.849][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.858][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [4781, 0, 4781, C29H40N2O4, InChI=1S/C29H40N2O4/c1-6-18-17-31-10-8-20-14-27(33-3)29(35-5)16-23(20)25(31)12-21(18)11-24-22-15-28(34-4)26(32-2)13-19(22)7-9-30-24/h13-16,18,21,24-25,30H,6-12,17H2,1-5H3/t18-,21-,24+,25-/m0/s1, ...]. biodb.DEBUG[2024-07-06 16:04:23.859][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:23.860][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:23.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:23.865][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:23.865][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:23.866][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:23.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:23.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:23.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:23.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:23.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:23.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.874][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.875][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:23.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:23.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.878][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.879][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:23.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:23.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.882][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.885][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.886][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.889][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.890][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.892][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.893][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.896][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.897][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.898][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.899][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.900][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.903][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.904][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.906][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.907][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.910][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.911][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.913][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.914][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.917][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.918][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.921][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.921][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.924][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.929][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.931][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.932][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.934][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.935][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.936][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.938][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.939][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.942][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.943][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:23.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:23.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.945][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.946][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.949][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.950][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:23.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:23.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.953][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.956][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.957][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:23.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.960][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:23.961][private$selectFields] biodb.TRACE[2024-07-06 16:04:23.962][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:23.963][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:23.964][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:23.965][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:23.966][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:23.966][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.967][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.968][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:23.969][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:23.970][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.971][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.972][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.973][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:23.973][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.974][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.975][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:23.976][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:23.977][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.978][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.979][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:23.980][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:23.980][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.981][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.982][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:23.983][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:23.984][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.985][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.986][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.986][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:23.987][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.988][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.989][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.990][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:23.991][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.992][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.993][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.994][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:23.994][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.995][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:23.996][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:23.997][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:23.998][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:23.999][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.000][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:24.001][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:24.001][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.002][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.003][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:24.004][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:24.005][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.006][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.007][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:24.008][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:24.008][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.009][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.010][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:24.011][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:24.012][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.013][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.014][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:24.015][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:24.015][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.016][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.017][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.018][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.019][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.020][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.021][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:24.022][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:24.022][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.023][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.024][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:24.030][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:24.031][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.032][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.033][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:24.034][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:24.035][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.036][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.037][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.038][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.039][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.039][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.040][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.041][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.042][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.043][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.044][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.045][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.046][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.046][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.047][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:24.048][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:24.049][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.050][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.051][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:24.052][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:24.052][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.053][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.054][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:24.055][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:24.056][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.057][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.058][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:24.058][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:24.059][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.060][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.061][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:24.062][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:24.063][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:24.064][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:24.065][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.065][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.066][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:24.067][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:24.068][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.069][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.070][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.071][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.071][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.072][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.073][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:24.074][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:24.075][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.076][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.077][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:24.077][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:24.078][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.079][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.080][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:24.081][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:24.082][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.083][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.083][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.084][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.085][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.086][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.087][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.088][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.089][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.089][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.090][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.091][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.092][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.093][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.094][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:24.095][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:24.095][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.096][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.097][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:24.098][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:24.099][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.100][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.101][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:24.102][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:24.102][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.103][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.104][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:24.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:24.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:24.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.108][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:24.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:24.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.111][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:24.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:24.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.115][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.116][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:24.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:24.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.118][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.119][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:24.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:24.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.123][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:24.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:24.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.125][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.126][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.130][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.133][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.136][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.137][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:24.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:24.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.141][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:24.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:24.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.144][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:24.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:24.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.147][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.148][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:24.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:24.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.151][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:24.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:24.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.155][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:24.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:24.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.159][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:24.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:24.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.162][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:24.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:24.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.166][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:24.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:24.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.169][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.173][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.177][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.180][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.184][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.187][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.191][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.195][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.198][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.202][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:24.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:24.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.205][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:24.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:24.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.209][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:24.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:24.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.213][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:24.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:24.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.216][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:24.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:24.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.220][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:24.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:24.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.223][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:24.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:24.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.227][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:24.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:24.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.230][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:24.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:24.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.239][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [16587, 0, 16587, C27H44O7, InChI=1S/C27H44O7/c1-23(2,32)9-8-22(31)26(5,33)21-7-11-27(34)16-12-18(28)17-13-19(29)20(30)14-24(17,3)15(16)6-10-25(21,27)4/h12,15,17,19-22,29-34H,6-11,13-14H2,1-5H3/t15-,17-,19+,20-,21-,22+,24+,25+,26+,27+/m0/s1, ...]. biodb.DEBUG[2024-07-06 16:04:24.240][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:24.241][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:24.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:24.246][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:24.247][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:24.247][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:24.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:24.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:24.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:24.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.253][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:24.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:24.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.256][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:24.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:24.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.260][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:24.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:24.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.263][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.271][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:24.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:24.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.274][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:24.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:24.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.278][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:24.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:24.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.280][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.281][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:24.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:24.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.285][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:24.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:24.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.288][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:24.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:24.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.292][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.295][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.299][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.311][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.312][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.314][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.315][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.318][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.319][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:24.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:24.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.322][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:24.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:24.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.326][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:24.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:24.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.329][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:24.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:24.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.333][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:24.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:24.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.336][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:24.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:24.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.340][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:24.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:24.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.343][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:24.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:24.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.347][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:24.348][private$selectFields] biodb.TRACE[2024-07-06 16:04:24.348][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:24.349][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:24.350][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:24.351][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:24.352][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:24.353][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.354][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.355][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:24.355][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:24.356][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.357][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.358][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.359][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.360][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.361][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.361][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:24.362][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:24.363][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.364][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.365][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:24.366][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:24.367][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.367][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.368][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:24.369][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:24.370][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.371][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.372][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.373][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.374][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.374][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.375][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.376][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.377][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.378][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.379][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.380][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.380][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.381][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.382][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:24.383][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:24.384][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.385][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.386][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:24.387][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:24.387][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.388][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.389][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:24.390][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:24.391][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.392][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.393][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:24.393][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:24.394][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.395][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.396][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:24.397][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:24.398][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.399][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.399][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:24.400][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:24.401][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.402][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.403][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.404][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.405][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.406][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.406][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:24.407][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:24.408][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.409][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.410][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:24.411][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:24.412][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.413][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.414][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:24.414][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:24.415][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.416][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.417][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.418][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.419][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.420][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.421][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.422][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.422][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.423][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.424][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.425][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.426][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.427][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.428][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:24.429][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:24.429][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.430][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.431][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:24.432][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:24.433][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.434][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.435][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:24.436][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:24.436][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.437][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.438][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:24.439][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:24.440][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.441][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.442][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:24.443][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:24.444][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:24.444][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:24.445][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.446][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.447][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:24.448][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:24.449][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.450][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.451][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.452][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.452][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.453][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.454][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:24.455][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:24.456][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.457][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.458][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:24.459][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:24.459][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.460][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.461][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:24.462][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:24.463][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.464][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.465][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.466][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.467][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.467][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.468][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.469][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.470][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.471][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.472][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:24.473][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:24.474][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.474][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.475][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:24.476][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:24.477][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.478][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.479][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:24.480][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:24.481][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.481][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.482][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:24.483][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:24.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:24.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.486][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.487][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:24.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:24.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.490][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:24.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:24.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.494][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:24.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:24.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.498][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:24.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:24.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.501][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:24.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:24.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.509][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.511][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.512][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.516][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:24.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:24.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.520][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:24.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:24.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.523][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:24.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:24.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.527][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:24.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:24.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.529][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.530][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:24.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:24.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.534][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:24.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:24.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:24.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:24.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:24.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:24.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:24.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:24.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.552][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.559][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.567][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.570][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:24.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:24.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.574][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:24.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:24.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.578][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:24.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:24.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.586][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:24.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:24.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:24.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:24.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.593][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.594][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:24.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:24.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.598][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:24.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:24.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.600][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.601][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:24.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:24.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.604][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.605][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:24.606][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:24.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.607][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.613][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [19804, 0, 19804, C27H44O7, InChI=1S/C27H44O7/c1-23(2,32)8-5-9-26(33,15-28)22-7-11-27(34)17-12-19(29)18-13-20(30)21(31)14-24(18,3)16(17)6-10-25(22,27)4/h12,16,18,20-22,28,30-34H,5-11,13-15H2,1-4H3/t16-,18-,20+,21-,22-,24+,25+,26+,27+/m0/s1, ...]. biodb.DEBUG[2024-07-06 16:04:24.614][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:24.615][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:24.617][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:24.618][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:24.619][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:24.623][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:24.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:24.625][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:24.625][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:24.628][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:24.631][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:24.632][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26d0872875c47c33e8205aa7124e0486". biodb.TRACE[2024-07-06 16:04:24.633][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:24.634][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26d0872875c47c33e8205aa7124e0486.content". biodb.DEBUG[2024-07-06 16:04:24.636][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:24.637][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:24.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:24.641][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:24.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:24.643][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:24.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:24.645][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:24.655][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:24.656][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:24.657][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:24.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:24.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:24.662][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:24.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:24.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.667][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.671][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.674][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:24.675][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:24.676][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:24.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:24.680][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:24.681][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:24.682][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:24.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:24.684][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.686][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.687][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.691][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:24.695][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:24.695][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:24.696][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:24.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:24.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:24.702][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:24.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:24.704][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.707][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:24.714][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:24.715][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:24.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:24.720][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:24.721][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:24.721][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:24.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:24.723][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.726][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.729][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.730][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:24.734][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:24.735][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:24.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:24.739][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:24.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:24.741][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:24.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:24.743][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.746][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.750][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:24.754][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:24.754][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:24.755][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:24.759][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:24.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:24.761][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:24.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:24.763][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.765][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.766][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.772][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:24.773][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:24.774][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:24.775][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:24.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:24.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:24.780][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:24.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:24.782][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.786][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.789][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:24.794][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:24.797][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:24.798][cch$loadFileContent] Trying to load 1 files from cache: [1]: "357534c211a0779cb44e196fcebae6c0". biodb.TRACE[2024-07-06 16:04:24.799][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:24.800][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/357534c211a0779cb44e196fcebae6c0.content". biodb.DEBUG[2024-07-06 16:04:24.802][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:24.803][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:24.804][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:24.808][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:24.809][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:24.810][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:24.810][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:24.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.818][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.818][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:24.822][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:24.823][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:24.824][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:24.828][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:24.828][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:24.829][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:24.830][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:24.831][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.835][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.838][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:24.842][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:24.842][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:24.843][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:24.847][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:24.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:24.849][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:24.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:24.851][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.854][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.858][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.866][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:24.867][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:24.869][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:24.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:24.870][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:24.874][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:24.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:24.876][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:24.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:24.878][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:24.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:24.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.880][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:24.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:24.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.884][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.885][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:24.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:24.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.888][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:24.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:24.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.892][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.899][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:24.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:24.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.902][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:24.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:24.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.906][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:24.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:24.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.908][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.909][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:24.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:24.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:24.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:24.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.915][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.916][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:24.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:24.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.920][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.923][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:24.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.941][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:24.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:24.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.944][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:24.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:24.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.947][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:24.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:24.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.951][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:24.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:24.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.954][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:24.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:24.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.958][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:24.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:24.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.961][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:24.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:24.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.965][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:24.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:24.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.968][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.969][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:24.969][private$selectFields] biodb.TRACE[2024-07-06 16:04:24.970][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:24.971][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:24.972][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:24.973][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:24.974][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:24.975][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.976][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.977][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:24.977][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:24.978][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.979][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.980][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.981][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:24.982][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.983][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.984][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:24.984][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:24.985][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.986][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.987][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:24.988][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:24.989][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.990][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.991][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:24.992][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:24.992][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.993][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.994][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.995][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:24.996][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:24.997][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:24.998][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.999][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:24.999][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.000][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.001][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.002][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.003][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.004][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.005][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.006][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.006][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.007][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.008][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.009][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.010][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.011][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.012][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.013][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.014][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.014][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.015][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.016][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.017][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.018][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.019][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.020][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.021][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.022][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.022][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.023][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.024][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.025][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.026][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.027][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.028][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.029][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.029][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.030][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.031][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.032][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.033][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.034][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.035][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.036][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.036][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.037][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.038][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.039][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.040][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.041][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.042][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.043][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.044][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.044][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.045][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.046][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.047][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.048][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.049][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.050][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.051][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.052][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.053][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.053][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.054][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.055][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.056][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.057][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.058][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.059][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.060][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.060][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.061][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.062][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.063][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.064][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.065][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:25.066][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:25.067][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.068][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.068][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.069][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.070][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.071][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.072][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.073][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.074][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.075][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.075][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.076][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.077][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.078][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.079][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.080][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.081][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.082][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.082][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.083][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.084][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.085][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.086][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.087][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.088][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.089][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.089][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.090][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.091][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.092][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.093][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.094][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.095][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.096][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.096][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.097][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.098][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.099][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.100][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.101][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.102][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.103][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.103][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.104][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.105][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.106][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.107][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.108][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.109][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:25.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.121][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.125][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.128][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.141][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.145][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.149][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.152][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.156][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.159][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.163][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.166][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.166][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.170][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.174][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.177][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.181][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.184][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.188][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.205][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.209][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.213][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.216][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.220][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.222][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.223][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.226][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.227][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.229][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.230][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.234][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.237][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.241][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.244][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.250][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [7799, 0, 7799, C16H31N2O8P, InChI=1S/C16H28N2O4.H3O4P/c1-5-12(6-2)22-14-9-11(16(20)21-7-3)8-13(17)15(14)18-10(4)19;1-5(2,3)4/h9,12-15H,5-8,17H2,1-4H3,(H,18,19);(H3,1,2,3,4)/t13-,14+,15+;/m0./s1, ...]. biodb.DEBUG[2024-07-06 16:04:25.251][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:25.252][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:25.252][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:25.256][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:25.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:25.258][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:25.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:25.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.264][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.267][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.271][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.273][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.274][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.277][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.278][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.281][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.281][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.285][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.288][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.292][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.296][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.298][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.299][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.303][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.305][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.306][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.310][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.314][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.321][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.325][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.327][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.328][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.331][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.334][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.335][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.338][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.339][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.341][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.342][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.345][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.346][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.349][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.349][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.352][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.353][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:25.354][private$selectFields] biodb.TRACE[2024-07-06 16:04:25.355][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:25.355][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:25.356][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:25.357][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.358][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.359][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.360][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.361][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.362][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.362][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.363][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.364][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.365][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.366][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.367][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.368][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.369][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.369][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.370][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.371][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.372][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.373][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.374][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.375][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.376][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.377][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.377][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.378][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.379][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.380][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.381][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.382][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.383][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.384][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.384][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.385][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.386][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.387][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.388][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.389][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.390][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.391][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.391][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.392][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.393][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.394][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.395][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.396][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.397][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.398][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.398][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.399][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.400][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.401][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.402][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.403][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.404][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.405][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.405][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.406][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.407][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.408][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.409][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.410][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.411][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.412][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.417][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.419][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.420][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.421][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.422][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.422][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.423][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.424][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.425][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.426][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.427][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.428][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.429][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.430][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.430][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.431][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.432][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.433][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.434][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.435][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.436][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.436][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.437][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.438][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.439][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.440][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.441][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.442][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.442][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.443][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.444][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.445][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.446][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.447][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.448][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.449][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.449][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.450][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.451][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.452][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.453][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.454][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:25.455][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:25.455][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.456][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.457][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.458][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.459][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.460][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.461][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.462][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.462][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.463][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.464][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.465][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.466][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.467][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.468][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.468][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.469][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.470][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.471][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.472][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.473][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.474][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.474][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.475][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.476][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.477][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.478][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.479][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.480][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.481][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.481][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.482][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.483][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.484][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.485][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.486][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.487][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.487][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.488][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.489][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.490][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.491][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.492][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.493][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.493][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:25.494][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.497][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.501][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.505][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.508][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.511][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.512][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.526][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.529][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.530][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.534][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.543][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.544][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.547][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.548][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.552][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.554][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.555][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.566][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.572][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.577][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.580][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.584][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.588][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.595][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.597][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.602][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.606][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.609][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.617][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [71954, 0, 71954, C18H21F3N6O2, InChI=1S/C18H21F3N6O2/c19-18(20,21)13-9-15(22)23-11-12(13)14-10-16(26-1-5-28-6-2-26)25-17(24-14)27-3-7-29-8-4-27/h9-11H,1-8H2,(H2,22,23), ...]. biodb.DEBUG[2024-07-06 16:04:25.618][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:25.619][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:25.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:25.624][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:25.625][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:25.626][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:25.626][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:25.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.631][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.635][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.637][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.638][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.642][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.645][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.649][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.652][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.655][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.656][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.659][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.660][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.663][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.667][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.670][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.674][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.681][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.684][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.684][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.697][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.700][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.701][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.704][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.706][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.707][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.708][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.711][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.714][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.715][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.718][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.721][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.722][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.725][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:25.726][private$selectFields] biodb.TRACE[2024-07-06 16:04:25.727][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:25.728][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:25.729][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:25.730][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.730][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.731][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.732][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.733][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.734][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.735][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.736][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.737][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.737][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.738][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.739][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.740][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.741][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.742][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.743][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.743][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.744][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.745][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.746][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.747][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.748][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.749][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.749][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.750][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.751][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.752][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.753][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.754][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.755][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.756][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.756][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.757][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.758][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.759][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.760][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.761][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.762][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.762][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.763][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.764][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.765][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.766][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.767][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.768][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.769][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.769][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.770][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.771][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.772][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.773][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.774][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.775][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.775][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.776][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.777][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.778][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.779][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.780][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.781][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.781][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.782][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.783][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.784][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.785][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.786][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.787][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.787][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.788][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.789][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.790][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.791][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.792][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.793][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.794][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.794][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.795][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.796][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:25.797][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.798][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.799][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.800][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.801][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.802][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.802][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.803][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.804][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.805][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.806][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.807][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.808][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.809][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.810][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.810][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.811][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.812][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.813][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.814][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.815][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.816][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.817][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.817][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:25.818][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.819][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.820][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:25.821][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:25.822][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.823][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.824][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.825][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.825][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.826][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.827][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.828][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.829][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.830][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.831][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.832][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.832][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.833][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.834][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.835][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.836][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.837][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.838][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.839][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.839][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.840][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.841][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.842][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.843][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.844][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.845][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.846][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.846][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.847][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.848][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.849][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.850][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.851][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.852][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.853][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.853][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.854][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.855][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.856][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.857][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.858][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.859][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.860][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.861][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:25.862][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:25.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:25.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.871][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.873][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.876][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.880][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:25.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:25.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.883][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.887][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.890][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:25.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.893][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.894][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.898][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.901][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:25.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:25.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.907][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.908][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.912][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:25.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:25.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.915][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.916][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.918][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.919][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.923][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:25.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:25.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.925][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.926][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.927][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.928][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.933][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:25.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.936][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.948][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.951][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.955][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:25.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:25.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.959][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.962][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.970][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.971][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:25.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:25.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.975][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.979][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.982][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.982][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:25.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:25.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:25.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:25.991][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [197612, 0, 197612, C18H18O9S, InChI=1S/C18H18O9S/c1-7-3-9(19)13-11(4-7)27-16-8(14(13)21)5-12(28-16)18(25,17(24)26-2)6-10(20)15(22)23/h3-4,10,12,19-20,25H,5-6H2,1-2H3,(H,22,23)/t10-,12+,18?/m1/s1, ...]. biodb.DEBUG[2024-07-06 16:04:25.992][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:25.992][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-07-06 16:04:25.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:25.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.000][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.001][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.004][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.005][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.014][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.021][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.022][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.028][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.035][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.036][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.039][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:26.042][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:26.043][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:26.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:26.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:26.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:26.049][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:26.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:26.053][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:26.056][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:26.057][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2024-07-06 16:04:26.058][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:26.059][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2024-07-06 16:04:26.062][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:26.065][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:26.066][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2024-07-06 16:04:26.067][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:26.068][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2024-07-06 16:04:26.070][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:26.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:26.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:26.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:26.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:26.077][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:26.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:26.079][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.082][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.083][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.086][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.087][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.089][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:26.090][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:26.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:26.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:26.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:26.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:26.097][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:26.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:26.099][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.103][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.106][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:26.110][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:26.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:26.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:26.116][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:26.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:26.118][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:26.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:26.119][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.122][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.126][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.127][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.129][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:26.130][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:26.132][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:26.133][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:26.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:26.137][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:26.138][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:26.139][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:26.140][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:26.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.147][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.148][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.152][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.154][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.155][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.159][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.163][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.166][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.170][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.173][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.177][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.181][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.184][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.188][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.191][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.195][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.198][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.199][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.202][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.206][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.209][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.213][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.217][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.220][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.224][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.227][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:26.228][private$selectFields] biodb.TRACE[2024-07-06 16:04:26.229][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:26.230][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:26.231][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:26.232][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.233][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.234][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.234][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.235][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.236][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.237][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.238][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.239][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.240][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.241][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.241][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.242][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.243][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.244][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.251][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.252][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.253][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.254][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.255][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.256][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.257][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.257][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.258][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.259][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.260][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.261][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.262][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.263][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.264][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.264][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.265][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.266][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.267][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.268][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.269][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.270][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.271][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.271][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.272][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.273][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.274][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.275][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.276][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.277][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.278][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.278][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.279][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.280][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.281][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.282][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.283][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.284][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.285][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.285][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.286][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.287][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.288][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.289][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.290][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.291][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.292][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.292][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.293][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.294][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.295][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.296][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.297][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.298][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.298][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.299][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.300][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.301][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.302][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.303][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.304][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.305][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.305][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.306][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.307][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.308][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.309][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.310][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.311][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.312][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.312][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.313][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.314][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.315][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.316][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.317][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.318][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.319][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.319][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.320][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.321][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.322][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:26.323][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:26.324][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.325][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.326][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.327][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.327][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.328][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.329][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.330][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.331][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.332][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.333][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.334][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.334][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.335][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.336][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.337][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.338][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.339][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.340][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.341][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.342][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.343][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.343][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.344][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.345][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.346][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.347][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.348][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.349][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.350][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.350][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.351][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.352][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.353][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.354][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.355][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.356][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.357][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.358][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.358][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.359][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.360][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.361][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.362][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.363][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.364][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.365][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.366][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.366][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:26.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.374][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.378][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.382][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.385][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.386][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.389][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.392][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.396][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.399][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.400][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.403][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.404][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.407][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.410][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.411][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.414][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.414][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.418][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.421][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.422][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.425][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.429][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.432][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.436][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.439][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.443][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.447][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.449][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.450][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.454][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.457][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.458][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.465][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.467][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.468][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.472][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.475][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.476][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.479][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.483][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.486][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.490][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.493][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.502][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [4648, 0, 4648, C30H50, InChI=1S/C30H50/c1-20(2)21-12-17-27(5)22(21)13-18-29(7)24(27)10-11-25-28(6)16-9-15-26(3,4)23(28)14-19-30(25,29)8/h21-25H,1,9-19H2,2-8H3/t21-,22+,23+,24-,25-,27+,28+,29-,30-/m1/s1, ...]. biodb.DEBUG[2024-07-06 16:04:26.503][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:26.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:26.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:26.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:26.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:26.510][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:26.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:26.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.515][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.516][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.519][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.519][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.527][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.528][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.531][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.536][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.539][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.543][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.546][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.550][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.553][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.557][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.560][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.564][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.567][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.571][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.574][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.578][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.582][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.585][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.589][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.592][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.596][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.599][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.603][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:26.603][private$selectFields] biodb.TRACE[2024-07-06 16:04:26.604][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:26.605][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:26.606][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:26.607][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.608][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.609][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.609][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.610][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.611][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.612][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.613][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.614][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.615][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.615][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.616][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.617][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.618][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.619][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.620][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.621][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.621][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.622][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.623][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.624][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.625][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.626][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.627][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.628][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.628][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.629][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.630][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.631][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.632][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.633][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.634][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.635][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.636][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.636][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.637][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.638][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.639][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.640][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.641][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.642][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.643][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.643][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.644][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.645][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.646][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.647][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.648][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.649][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.650][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.651][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.651][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.652][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.653][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.654][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.655][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.656][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.657][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.658][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.658][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.659][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.660][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.661][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.662][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.663][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.664][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.665][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.666][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.666][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.667][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.668][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.669][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.670][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.671][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.672][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.673][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.673][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.674][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.675][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.676][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.677][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.678][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.679][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.680][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.680][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.681][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.682][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.683][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.684][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.685][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.686][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.687][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.687][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.688][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.689][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.690][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.691][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:26.692][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:26.693][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.694][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.695][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.695][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.696][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.697][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.698][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.699][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.700][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.701][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.702][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.702][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.703][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.704][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.705][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.706][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.707][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.708][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.709][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.709][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.710][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.711][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.712][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.713][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.714][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.715][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.716][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.716][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.717][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.718][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.719][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.720][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.721][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.722][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.723][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.723][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.724][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.725][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.726][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.727][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.728][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.729][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.730][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.730][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.731][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.732][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.733][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.734][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.735][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:26.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.739][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.742][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.743][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.747][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.750][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.754][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.757][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.767][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.768][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.772][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.774][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.775][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.779][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.782][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.786][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.790][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.793][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.802][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.806][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.810][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.813][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.817][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.820][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.820][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.824][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.828][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.831][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.835][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.835][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.838][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.842][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.844][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.845][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.849][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.851][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.855][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.856][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.858][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.859][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.862][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.863][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.865][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.866][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.869][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.875][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [15440, 0, 15440, C30H50, InChI=1S/C30H50/c1-25(2)15-11-19-29(7)23-13-21-27(5)17-9-10-18-28(6)22-14-24-30(8)20-12-16-26(3)4/h15-18,23-24H,9-14,19-22H2,1-8H3/b27-17+,28-18+,29-23+,30-24+, ...]. biodb.DEBUG[2024-07-06 16:04:26.876][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:26.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:26.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:26.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:26.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:26.883][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:26.884][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:26.885][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.887][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.888][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.891][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.892][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.895][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.898][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.899][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.902][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.902][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.905][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.906][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.909][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.910][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.912][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.913][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.916][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.917][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.920][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.924][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.927][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.930][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.931][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.935][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.938][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:26.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.942][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:26.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.949][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.952][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:26.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:26.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.956][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.959][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:26.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:26.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.963][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.967][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:26.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:26.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.970][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:26.971][private$selectFields] biodb.TRACE[2024-07-06 16:04:26.972][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:26.973][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:26.974][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:26.974][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:26.975][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:26.976][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.977][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.978][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:26.979][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:26.980][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.981][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.982][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.982][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:26.983][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.984][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.985][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:26.986][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:26.987][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.988][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.989][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:26.990][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:26.990][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.991][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.992][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:26.993][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:26.994][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.995][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.996][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.997][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:26.997][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:26.998][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:26.999][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.000][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.001][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.002][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.003][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.004][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.004][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.005][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.006][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.007][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.008][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.009][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.010][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.011][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.011][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.012][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.013][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.014][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.015][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.016][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.017][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.018][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.019][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.019][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.020][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.021][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.022][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.023][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.024][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.025][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.026][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.026][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.027][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.028][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.029][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.030][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.031][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.032][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.033][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.033][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.034][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.035][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.036][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.037][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.038][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.039][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.040][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.041][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.041][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.042][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.043][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.044][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.045][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.046][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.047][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.048][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.048][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.049][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.050][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.051][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.052][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.053][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.054][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.055][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.056][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.056][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.057][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.058][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.059][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:27.060][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:27.061][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.062][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.063][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.064][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.064][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.065][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.066][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.067][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.068][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.069][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.070][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.071][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.077][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.078][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.079][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.080][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.081][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.082][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.083][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.084][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.084][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.085][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.086][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.087][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.088][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.089][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.090][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.091][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.092][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.092][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.093][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.094][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.095][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.096][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.097][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.098][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.098][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.099][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.100][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.101][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.102][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.103][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.104][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.104][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.105][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:27.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.110][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.112][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.113][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.117][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.120][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.124][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.128][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.131][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.135][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.138][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.141][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.142][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.145][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.148][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.149][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.151][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.152][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.155][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.156][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.158][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.159][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.162][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.163][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.165][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.166][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.169][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.173][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.173][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.192][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.195][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.198][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.199][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.202][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.206][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.209][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.213][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.217][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.220][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.229][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [62447, 0, 62447, C30H50, InChI=1S/C30H50/c1-21(2)11-9-12-22(3)23-15-19-29(7)24(23)13-14-26-28(6)18-10-17-27(4,5)25(28)16-20-30(26,29)8/h11,23-26H,3,9-10,12-20H2,1-2,4-8H3/t23-,24-,25+,26-,28+,29-,30-/m1/s1, ...]. biodb.DEBUG[2024-07-06 16:04:27.230][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:27.230][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:27.233][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:27.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:27.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:27.239][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:27.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:27.240][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:27.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:27.244][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.29*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:27.246][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:27.248][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7269bbea581f1e243800f8ee4e0f4fdb". biodb.TRACE[2024-07-06 16:04:27.249][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:27.250][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7269bbea581f1e243800f8ee4e0f4fdb.content". biodb.DEBUG[2024-07-06 16:04:27.252][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:27.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:27.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:27.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:27.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:27.259][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:27.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:27.261][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.265][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:27.272][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:27.273][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:27.273][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:27.277][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:27.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:27.279][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:27.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:27.281][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.284][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.288][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.291][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:27.292][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:27.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:27.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:27.297][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:27.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:27.299][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:27.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:27.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.303][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.307][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.308][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:27.311][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:27.313][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:27.314][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:27.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:27.318][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:27.319][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:27.320][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:27.321][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:27.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.325][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.329][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.333][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.340][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.343][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.347][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.356][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.360][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.364][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.367][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.371][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.374][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.378][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.381][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.392][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.395][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.399][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.401][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.402][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.406][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.409][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.412][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.413][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:27.414][private$selectFields] biodb.TRACE[2024-07-06 16:04:27.414][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:27.415][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:27.416][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:27.417][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.418][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.419][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.420][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.420][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.421][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.422][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.423][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.424][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.425][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.426][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.427][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.427][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.428][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.429][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.430][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.431][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.432][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.433][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.433][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.434][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.435][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.436][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.437][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.438][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.439][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.440][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.440][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.441][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.442][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.443][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.444][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.445][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.446][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.447][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.447][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.448][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.449][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.450][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.451][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.452][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.453][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.454][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.454][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.455][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.456][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.457][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.458][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.459][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.460][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.461][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.462][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.462][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.463][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.464][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.465][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.466][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.467][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.468][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.469][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.470][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.470][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.471][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.472][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.473][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.474][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.475][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.476][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.477][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.478][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.478][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.479][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.480][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.481][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.482][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.483][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.484][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.485][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.485][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.486][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.487][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.488][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.489][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.490][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.491][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.492][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.492][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.493][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.494][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.495][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.496][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.497][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.498][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.499][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.499][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.500][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.501][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:27.502][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:27.503][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.504][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.505][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.506][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.506][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.507][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.508][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.509][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.510][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.511][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.512][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.513][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.513][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.514][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.515][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.516][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.517][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.518][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.519][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.520][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.520][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.521][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.522][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.523][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.524][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.525][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.526][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.527][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.527][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.528][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.529][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.530][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.531][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.532][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.533][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.534][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.534][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.535][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.536][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.537][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.538][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.539][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.540][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.541][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.541][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.542][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.543][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.544][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.545][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:27.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.553][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.557][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.559][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.560][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.564][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.568][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.571][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.575][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.578][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.582][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.585][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.592][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.593][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.596][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.600][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.603][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.603][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.607][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.610][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.611][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.614][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.617][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.618][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.621][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.631][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.635][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.639][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.642][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.645][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.646][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.648][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.649][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.652][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.653][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.655][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.656][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.659][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.660][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.663][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.663][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.666][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.670][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.671][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.674][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.677][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.678][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.686][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [4781, 0, 4781, C29H40N2O4, InChI=1S/C29H40N2O4/c1-6-18-17-31-10-8-20-14-27(33-3)29(35-5)16-23(20)25(31)12-21(18)11-24-22-15-28(34-4)26(32-2)13-19(22)7-9-30-24/h13-16,18,21,24-25,30H,6-12,17H2,1-5H3/t18-,21-,24+,25-/m0/s1, ...]. biodb.DEBUG[2024-07-06 16:04:27.687][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:27.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:27.689][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:27.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:27.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:27.695][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:27.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:27.696][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.700][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.703][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.706][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.707][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.710][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.710][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.713][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.714][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.717][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.717][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.721][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.724][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.724][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.728][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.731][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.732][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.735][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.738][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.739][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.742][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.746][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.749][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.753][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.757][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.760][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.764][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.767][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.774][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.778][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.781][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.781][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:27.782][private$selectFields] biodb.TRACE[2024-07-06 16:04:27.783][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:27.784][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:27.785][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:27.786][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.787][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.788][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.788][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.789][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.790][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.791][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.792][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.793][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.794][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.795][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.795][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.796][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.797][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.798][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.799][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.800][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.801][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.802][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.802][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.803][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.804][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.805][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.806][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.807][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.808][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.809][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.809][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.810][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.811][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.812][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.813][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.814][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.815][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.816][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.816][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.817][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.818][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.819][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.820][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.821][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.822][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.823][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.823][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.824][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.825][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.826][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.827][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.828][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.829][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.830][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.830][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.831][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.832][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.833][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.834][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.835][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.836][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.837][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.837][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.838][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.839][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.840][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.841][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.842][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.843][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.844][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.845][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.845][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.846][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.847][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.848][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.849][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.850][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:27.851][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.851][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.852][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.853][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.854][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.855][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.856][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.857][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.858][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.858][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.859][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.860][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.861][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.862][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.863][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.864][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.865][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.865][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.866][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.867][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.868][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.869][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.870][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:27.871][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:27.872][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.873][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.873][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.874][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.875][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.876][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.877][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.878][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.879][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.880][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.880][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.881][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.882][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.883][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.884][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.885][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.886][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.887][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.887][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.888][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.889][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.890][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.891][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.892][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.893][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.894][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.894][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.895][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.896][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.902][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.903][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.904][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.905][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:27.906][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:27.907][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.908][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.909][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:27.910][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:27.911][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.912][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.912][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:27.913][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:27.914][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.915][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.916][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:27.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.923][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:27.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:27.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.927][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.928][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.930][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.931][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.934][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.935][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:27.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:27.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.938][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.941][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.942][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.945][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:27.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.948][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.949][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.952][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.952][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.955][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.956][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:27.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:27.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.959][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.960][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.963][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.966][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:27.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:27.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.970][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.974][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.977][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:27.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:27.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.981][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.984][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.988][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:27.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.991][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:27.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:27.998][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:27.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.002][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.006][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.009][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.013][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.016][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.020][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.024][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.027][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.031][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.039][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [91601, 0, 91601, C29H40N2O4, InChI=1S/C29H40N2O4/c1-6-18-17-31-10-8-20-14-27(33-3)29(35-5)16-23(20)25(31)12-21(18)11-24-22-15-28(34-4)26(32-2)13-19(22)7-9-30-24/h13-16,18,21,24-25,30H,6-12,17H2,1-5H3/t18-,21-,24?,25?/m0/s1, ...]. biodb.DEBUG[2024-07-06 16:04:28.040][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:28.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:28.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:28.046][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:28.047][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:28.047][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:28.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:28.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.056][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.057][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.060][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.064][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.071][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.074][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.078][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.081][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.081][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.085][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.088][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.089][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.092][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.096][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.099][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.103][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.105][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.109][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.110][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.113][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.113][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.116][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.117][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.120][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.121][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.123][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.124][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.127][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.128][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.130][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.131][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.134][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.135][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:28.136][private$selectFields] biodb.TRACE[2024-07-06 16:04:28.136][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:28.137][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:28.138][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:28.139][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.140][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.141][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.142][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.143][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.143][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.144][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.145][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.146][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.147][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.148][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.149][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.150][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.151][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.151][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.152][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.153][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.154][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.155][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.156][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.157][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.158][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.158][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.159][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.160][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.161][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.162][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.163][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.164][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.165][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.165][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.166][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.167][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.168][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.169][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.170][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.171][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.189][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.190][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.191][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.192][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.193][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.194][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.195][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.196][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.197][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.197][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.198][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.199][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.200][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.201][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.202][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.203][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.204][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.205][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.205][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.206][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.207][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.208][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.209][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.210][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.211][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.211][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.212][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.213][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.214][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.215][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.216][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.217][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.218][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.218][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.219][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.220][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.221][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.222][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.223][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.224][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.224][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.225][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.226][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.227][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.228][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.229][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.230][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.231][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.231][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.232][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.233][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.234][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.235][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.236][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.237][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.238][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.238][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.239][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.240][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.241][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:28.242][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:28.243][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.244][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.245][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.245][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.246][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.247][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.248][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.249][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.250][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.251][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.251][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.252][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.253][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.254][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.255][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.256][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.257][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.258][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.258][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.259][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.260][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.261][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.262][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.263][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.263][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.264][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.265][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.266][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.267][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.268][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.269][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.270][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.270][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.271][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.272][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.273][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.274][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.275][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.276][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.276][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.277][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.278][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.279][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.280][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.281][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:28.282][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.284][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.288][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.289][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.292][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.293][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.295][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.296][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.299][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.300][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.304][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.314][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.318][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.321][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.322][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.324][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.325][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.328][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.329][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.332][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.332][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.335][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.336][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.339][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.340][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.342][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.343][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.346][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.350][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.351][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.354][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.354][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.357][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.361][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.362][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.368][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.369][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.373][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.375][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.376][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.379][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.380][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.384][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.386][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.387][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.391][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.395][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.398][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.401][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.407][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [95147, 0, 95147, C29H40N2O4, InChI=1S/C29H40N2O4/c1-3-18-16(2)14-22-20(18)10-11-21-19-6-4-8-26(33)30-13-5-7-24-28(34)27(29(35)31-24)25(32)12-9-17(19)15-23(21)22/h4,8,10-11,16-24,27H,3,5-7,9,12-15H2,1-2H3,(H,30,33)(H,31,35)/t16-,17-,18-,19+,20+,21-,22+,23+,24+,27?/m1/s1, ...]. biodb.DEBUG[2024-07-06 16:04:28.408][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:28.409][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:28.412][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:28.412][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:28.413][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:28.417][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:28.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:28.419][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:28.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:28.422][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:28.425][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:28.426][cch$loadFileContent] Trying to load 1 files from cache: [1]: "acfa4b558978abf12409c2b56e678d03". biodb.TRACE[2024-07-06 16:04:28.428][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:28.429][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/acfa4b558978abf12409c2b56e678d03.content". biodb.DEBUG[2024-07-06 16:04:28.431][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:28.432][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:28.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:28.437][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:28.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:28.439][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:28.439][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:28.440][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.443][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.444][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.447][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.448][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.450][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:28.451][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:28.452][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:28.453][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:28.457][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:28.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:28.459][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:28.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:28.461][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.470][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.473][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.474][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:28.477][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:28.478][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:28.479][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:28.483][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:28.484][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:28.485][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:28.485][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:28.486][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.490][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.494][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:28.497][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:28.499][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:28.499][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:28.500][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:28.504][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:28.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:28.506][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:28.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:28.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.510][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.511][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.515][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.518][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.521][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.522][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.528][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.529][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.532][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.535][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.536][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.539][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.542][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.543][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.546][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.546][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.549][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.550][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.553][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.554][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.557][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.561][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.564][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.567][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.568][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.571][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.574][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.575][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.578][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.585][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.585][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.589][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.592][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.593][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:28.593][private$selectFields] biodb.TRACE[2024-07-06 16:04:28.594][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:28.595][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:28.596][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:28.597][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.598][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.599][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.600][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.600][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.601][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.602][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.603][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.604][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.605][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.606][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.607][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.608][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.608][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.609][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.610][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.611][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.612][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.613][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.614][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.615][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.616][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.616][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.617][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.618][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.619][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.620][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.621][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.622][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.623][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.623][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.624][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.625][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.626][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.627][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.628][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.629][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.630][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.630][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.631][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.632][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.633][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.634][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.635][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.636][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.637][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.637][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.638][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.639][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.640][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.641][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.642][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.643][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.644][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.644][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.645][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.646][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.647][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.648][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.649][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.650][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.651][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.651][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.652][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.653][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.654][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.655][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.656][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.657][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.658][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.659][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.659][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.660][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.661][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.662][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.663][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.664][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.665][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.666][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.666][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.667][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.668][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.669][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.670][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.671][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.672][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.673][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.674][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.674][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.675][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.676][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.677][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.678][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.679][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.680][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.681][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.682][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:28.682][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:28.683][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.684][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.685][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.686][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.687][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.688][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.689][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.689][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.690][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.691][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.692][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.693][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.694][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.695][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.696][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.697][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.697][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.698][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.699][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.700][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.701][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.702][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.703][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.704][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.704][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.705][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.706][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.707][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.708][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.709][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.710][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.711][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.711][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.712][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.713][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.714][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.715][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.716][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.717][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.718][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.719][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.719][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.720][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.721][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.722][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.723][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.724][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.725][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.726][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:28.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.729][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.730][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.733][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.736][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.738][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.740][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.746][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.749][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.750][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.753][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.754][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.757][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.758][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.760][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.764][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.765][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.768][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.769][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.771][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.772][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.775][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.776][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.778][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.779][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.782][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.783][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.785][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.786][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.789][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.790][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.792][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.793][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.796][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.797][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.800][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.800][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.804][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.807][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.808][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.811][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.815][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.818][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.824][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.825][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.829][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.831][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.832][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.835][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.836][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.838][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.839][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.842][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.843][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.847][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.849][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.850][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.853][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.854][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.858][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.860][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.866][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [636, 0, 636, C24H26O6, InChI=1S/C24H26O6/c1-12(2)6-7-14-19-17(11-16(26)22(14)28-5)29-18-10-15(25)13-8-9-24(3,4)30-23(13)20(18)21(19)27/h6,10-11,25-26H,7-9H2,1-5H3, ...]. biodb.DEBUG[2024-07-06 16:04:28.867][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:28.868][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:28.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:28.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:28.874][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:28.875][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:28.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:28.877][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.883][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.884][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.887][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.891][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.894][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.895][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.898][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.901][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.902][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.905][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.908][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.909][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.912][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.915][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.916][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.919][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.920][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.922][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.923][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.926][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.927][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.929][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.930][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.933][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.934][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.937][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.937][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.941][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.945][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:28.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.948][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.951][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.952][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:28.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:28.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.955][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.959][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:28.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:28.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.962][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:28.963][private$selectFields] biodb.TRACE[2024-07-06 16:04:28.964][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:28.965][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:28.966][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:28.967][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:28.968][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:28.968][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.969][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.970][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:28.971][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:28.972][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.973][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.974][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.975][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:28.975][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.976][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.977][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:28.978][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:28.979][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.980][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.981][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:28.982][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:28.982][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.983][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.984][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:28.985][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:28.986][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.987][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.988][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.989][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:28.989][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.990][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.991][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.992][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:28.993][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.994][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.995][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.996][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:28.996][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:28.997][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:28.998][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:28.999][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.000][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.001][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.002][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.003][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.003][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.004][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.005][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.006][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.007][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.008][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.009][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.010][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.011][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.011][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.012][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.013][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.014][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.015][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.016][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.017][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.023][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.024][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.025][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.026][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.027][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.027][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.028][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.029][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.030][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.031][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.032][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.033][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.034][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.035][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.036][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.036][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.037][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.038][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.039][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.040][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.041][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.042][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.042][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.043][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.044][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.045][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.046][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.047][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.048][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.049][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.049][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.050][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.051][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.052][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.053][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.054][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.055][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.055][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.056][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:29.057][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:29.058][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.059][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.060][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.061][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.062][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.063][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.063][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.064][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.065][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.066][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.067][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.068][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.068][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.069][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.070][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.071][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.072][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.073][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.074][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.075][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.075][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.076][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.077][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.078][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.079][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.080][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.081][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.081][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.082][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.083][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.084][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.085][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.086][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.087][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.087][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.088][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.089][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.090][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.091][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.092][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.093][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.093][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.094][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.095][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.096][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:29.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.100][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.103][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.107][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.108][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.110][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.111][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.114][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.115][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.118][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.125][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.129][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.132][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.133][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.136][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.140][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.143][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.143][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.147][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.150][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.151][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.154][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.157][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.158][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.161][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.162][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.164][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.169][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.171][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.172][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.176][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.182][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.183][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.187][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.189][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.190][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.193][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.194][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.197][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.200][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.201][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.204][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.205][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.208][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.211][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.212][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.220][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [64199, 0, 64199, C24H27ClN2O2, InChI=1S/C24H26N2O2.ClH/c27-24(28)20-9-10-23-22(16-20)21(17-25-23)8-4-5-13-26-14-11-19(12-15-26)18-6-2-1-3-7-18;/h1-3,6-7,9-11,16-17,25H,4-5,8,12-15H2,(H,27,28);1H, ...]. biodb.DEBUG[2024-07-06 16:04:29.221][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:29.222][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:29.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:29.227][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:29.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:29.228][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:29.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:29.230][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.233][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.234][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.236][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.237][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.240][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.241][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.243][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.244][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.247][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.251][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.251][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.254][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.255][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.258][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.259][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.261][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.262][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.265][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.266][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.268][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.269][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.272][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.273][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.276][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.279][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.283][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.286][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.287][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.290][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.299][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.300][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.302][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.303][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.306][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.307][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.310][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.310][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.313][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.314][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.317][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.318][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.320][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.321][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:29.322][private$selectFields] biodb.TRACE[2024-07-06 16:04:29.323][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:29.324][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:29.324][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:29.325][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.326][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.327][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.328][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.329][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.330][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.331][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.331][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.332][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.333][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.334][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.335][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.336][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.337][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.337][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.338][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.339][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.340][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.341][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.342][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.343][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.344][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.344][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.345][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.346][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.347][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.348][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.349][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.349][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.350][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.351][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.352][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.353][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.354][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.355][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.356][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.356][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.357][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.358][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.359][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.360][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.361][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.362][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.362][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.363][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.364][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.365][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.366][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.367][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.368][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.369][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.369][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.370][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.371][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.376][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.378][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.379][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.380][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.381][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.382][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.383][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.384][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.385][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.386][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.387][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.388][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.389][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.390][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.391][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.392][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.393][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.394][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.395][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.396][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.397][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.398][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.399][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.400][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.401][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.402][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.404][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.405][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.406][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.407][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.408][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.409][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.410][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.411][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.412][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.413][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.414][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.416][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.417][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.418][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.419][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.420][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.421][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:29.422][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:29.423][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.424][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.425][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.426][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.427][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.428][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.429][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.430][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.431][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.432][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.433][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.434][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.435][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.437][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.438][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.438][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.439][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.441][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.442][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.443][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.444][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.445][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.446][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.447][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.448][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.449][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.450][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.451][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.452][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.453][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.454][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.455][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.456][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.457][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.458][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.459][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.460][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.461][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.462][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.463][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.464][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.465][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.466][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.467][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.468][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:29.469][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.472][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.473][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.481][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.484][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.485][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.488][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.489][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.492][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.497][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.501][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.505][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.508][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.509][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.512][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.513][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.517][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.521][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.524][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.525][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.528][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.529][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.532][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.533][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.537][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.545][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.552][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.553][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.556][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.557][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.560][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.561][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.564][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.565][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.568][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.569][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.571][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.572][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.575][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.576][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.579][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.580][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.584][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.588][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.592][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.596][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.621][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [65648, 0, 65648, C24H26O6, InChI=1S/C24H26O6/c1-13(2)9-10-23-20(27)22(28-5)11-14-19(26)18-15(25)7-6-8-16(18)29-24(14,23)17(12-22)21(3,4)30-23/h6-9,11,17,25H,10,12H2,1-5H3/t17-,22-,23-,24+/m0/s1, ...]. biodb.DEBUG[2024-07-06 16:04:29.622][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:29.623][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:29.632][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:29.633][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:29.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:29.638][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:29.639][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:29.639][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:29.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:29.643][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:29.646][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:29.647][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386". biodb.TRACE[2024-07-06 16:04:29.648][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:29.650][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content". biodb.DEBUG[2024-07-06 16:04:29.653][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:29.656][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:29.657][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f". biodb.TRACE[2024-07-06 16:04:29.658][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:29.660][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content". biodb.DEBUG[2024-07-06 16:04:29.662][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:29.663][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:29.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:29.668][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:29.669][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:29.670][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:29.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:29.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.674][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.675][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.678][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.679][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.682][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:29.683][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:29.684][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:29.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:29.689][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:29.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:29.691][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:29.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:29.693][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.696][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.697][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.699][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.703][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:29.704][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:29.705][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:29.706][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:29.710][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:29.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:29.711][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:29.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:29.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.716][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.719][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:29.724][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:29.725][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:29.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:29.727][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:29.731][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:29.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:29.733][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:29.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:29.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.738][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.742][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.745][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.748][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.753][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.756][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.760][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.763][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.767][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.770][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.774][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.778][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.781][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.785][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.788][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.795][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.799][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.802][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.803][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.806][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.810][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.813][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.813][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.817][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.820][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.821][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:29.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:29.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.824][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:29.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:29.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.827][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.828][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:29.829][private$selectFields] biodb.TRACE[2024-07-06 16:04:29.829][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:29.830][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:29.831][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:29.832][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.833][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.834][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.835][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.835][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.836][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.837][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.838][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.839][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.840][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.841][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.842][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.842][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.843][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.844][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.845][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.846][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.847][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.848][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.849][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.849][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.850][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.851][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.852][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.853][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.854][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.855][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.856][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.857][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.857][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.858][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.859][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.860][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.861][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.862][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.863][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.864][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.865][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.865][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.866][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.867][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.868][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.869][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.870][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.871][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.872][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.872][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.873][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.874][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:29.875][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:29.876][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.877][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.878][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.879][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.879][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.880][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.881][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.882][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.883][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.884][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.885][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.886][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.886][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.887][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.888][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.889][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.890][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.891][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.892][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.893][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.894][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.894][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.895][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.902][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.903][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.904][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.905][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.906][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.907][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.907][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.908][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.909][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.910][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.911][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.912][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.913][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.914][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.915][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.915][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.916][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.917][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.918][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.919][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.920][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.921][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.921][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.922][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.923][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.924][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.925][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.926][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:29.927][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:29.928][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.928][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.929][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:29.930][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:29.931][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.932][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.933][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.934][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.935][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.935][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.936][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.937][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.938][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.939][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.940][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.941][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.941][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:29.942][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:29.943][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.944][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.945][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:29.946][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:29.947][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.947][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.948][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:29.949][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:29.950][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.951][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.952][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.953][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:29.954][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.954][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.955][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.956][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:29.957][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.958][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.959][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.960][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:29.960][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.961][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.962][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:29.963][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:29.964][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.965][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.966][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:29.967][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:29.967][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.968][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.969][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:29.970][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:29.971][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.972][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.973][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:29.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.977][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.980][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:29.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:29.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.984][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.988][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.991][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:29.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:29.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.995][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:29.997][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:29.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:29.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.002][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.006][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.008][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.009][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.013][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.016][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.020][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.024][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.026][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.027][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.031][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.033][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.034][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.038][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.042][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.044][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.045][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.049][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.052][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.060][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.062][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.063][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.069][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.070][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.073][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.074][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.077][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.078][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.080][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.081][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.084][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.085][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.087][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.088][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.091][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.092][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.095][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.096][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.098][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.099][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.102][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.108][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [4648, 0, 4648, C30H50, InChI=1S/C30H50/c1-20(2)21-12-17-27(5)22(21)13-18-29(7)24(27)10-11-25-28(6)16-9-15-26(3,4)23(28)14-19-30(25,29)8/h21-25H,1,9-19H2,2-8H3/t21-,22+,23+,24-,25-,27+,28+,29-,30-/m1/s1, ...]. biodb.DEBUG[2024-07-06 16:04:30.109][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:30.110][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:30.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:30.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:30.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:30.116][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:30.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:30.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.125][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.128][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.129][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.131][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.132][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.135][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.139][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.139][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.142][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.143][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.146][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.147][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.149][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.150][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.153][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.154][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.157][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.161][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.164][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.167][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.168][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.176][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.180][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.181][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.184][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.187][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.188][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.192][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.195][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.198][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.198][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.202][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.205][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.206][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.207][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.209][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:30.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:30.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.212][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:30.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:30.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.215][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.216][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:30.217][private$selectFields] biodb.TRACE[2024-07-06 16:04:30.218][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:30.218][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:30.219][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:30.220][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.221][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.222][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.223][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.224][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.225][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.225][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.226][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.227][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.228][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.229][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.230][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.231][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.232][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.232][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.233][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.234][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.235][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.236][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.237][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.238][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.238][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.239][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.240][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.241][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.242][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.243][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.244][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.244][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.245][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.246][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.247][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.248][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.249][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.250][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.251][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.251][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.252][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.253][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.254][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.255][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.256][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.257][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.257][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.258][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.259][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.260][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.261][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.262][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:30.263][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:30.264][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.264][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.265][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.266][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.267][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.268][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.269][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.270][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.271][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.271][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.272][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.273][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.274][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.275][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.276][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.277][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.278][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.278][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.279][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.280][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.281][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.282][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.283][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.284][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.285][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.286][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.286][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.287][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.288][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.289][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.290][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.291][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.292][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.293][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.293][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.294][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.295][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.296][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.297][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.298][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.299][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.300][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.301][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.302][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.302][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.303][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.304][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.305][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.306][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.307][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.308][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:30.309][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:30.309][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.310][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.311][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:30.312][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:30.313][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.314][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.315][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.316][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.317][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.318][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.318][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.319][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.320][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.321][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.322][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.323][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.324][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.325][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.325][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.326][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.327][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.328][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.329][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.330][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.331][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.332][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.333][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.333][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.334][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.335][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.336][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.337][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.338][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.339][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.340][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.340][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.341][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.342][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.343][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.344][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.345][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.346][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.347][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.347][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.348][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.349][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.350][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.351][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.352][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.353][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.354][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.354][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.355][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:30.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.359][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.363][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.363][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.366][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.367][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.370][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.371][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.373][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.374][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.377][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.381][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.381][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.384][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.385][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.388][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.389][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.391][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.392][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.395][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.396][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.398][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.399][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.402][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.403][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.406][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.407][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.409][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.410][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.413][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.414][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.416][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.417][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.420][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.421][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.425][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.427][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.428][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.431][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.432][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.434][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.435][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.436][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.438][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.439][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.443][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.445][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.455][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.456][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.458][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.459][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.462][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.463][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.466][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.466][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.469][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.470][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.473][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.474][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.476][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.477][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.480][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.481][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.483][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.484][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.487][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.488][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.490][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.496][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [15440, 0, 15440, C30H50, InChI=1S/C30H50/c1-25(2)15-11-19-29(7)23-13-21-27(5)17-9-10-18-28(6)22-14-24-30(8)20-12-16-26(3)4/h15-18,23-24H,9-14,19-22H2,1-8H3/b27-17+,28-18+,29-23+,30-24+, ...]. biodb.DEBUG[2024-07-06 16:04:30.497][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:30.498][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:30.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:30.503][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:30.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:30.505][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:30.505][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:30.506][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.509][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.510][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.513][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.513][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.516][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.517][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.520][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.520][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.523][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.526][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.527][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.530][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.531][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.534][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.537][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.538][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.541][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.548][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.548][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.551][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.552][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.555][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.556][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.558][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.562][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.563][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.565][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.566][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.569][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.570][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.574][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.576][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.577][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.580][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.581][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.583][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.584][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.588][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.591][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:30.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:30.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.595][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:30.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:30.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.599][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:30.599][private$selectFields] biodb.TRACE[2024-07-06 16:04:30.600][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:30.601][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:30.602][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:30.603][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.604][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.605][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.606][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.606][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.607][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.608][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.609][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.610][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.611][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.612][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.613][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.613][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.614][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.615][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.616][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.617][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.618][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.619][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.620][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.621][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.621][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.622][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.623][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.624][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.625][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.626][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.627][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.628][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.629][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.629][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.630][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.631][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.632][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.633][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.634][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.635][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.636][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.636][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.637][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.638][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.639][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.640][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.641][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.642][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.643][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.644][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.644][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.645][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:30.646][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:30.647][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.648][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.649][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.650][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.651][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.652][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.652][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.653][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.654][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.655][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.656][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.657][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.658][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.659][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.659][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.660][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.661][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.662][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.663][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.664][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.665][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.666][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.667][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.667][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.668][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.669][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.670][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.671][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:30.672][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.673][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.674][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.675][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.675][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.676][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.677][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.678][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.679][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.680][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.681][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.682][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.682][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.683][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.684][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.685][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.686][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.687][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.688][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.689][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.689][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.690][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.691][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:30.692][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:30.693][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.694][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.695][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:30.696][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:30.696][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.697][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.698][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.699][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.700][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.701][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.702][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.703][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.703][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.704][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.705][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.706][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.707][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.708][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.709][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.710][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.711][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.711][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.712][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.713][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.714][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.715][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.716][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.717][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.718][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.719][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.719][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.720][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.727][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.728][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.729][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.730][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.730][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.731][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.732][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.733][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.734][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.735][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.736][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.737][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.738][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.739][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.739][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.740][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.741][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:30.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.745][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.746][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.748][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.749][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.753][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.756][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.756][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.760][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.763][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.764][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.767][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.770][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.771][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.774][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.777][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.778][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.781][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.785][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.788][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.792][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.795][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.799][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.802][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.806][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.809][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.810][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.812][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.813][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:30.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.816][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.817][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.818][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.819][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.820][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.821][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.822][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.823][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.824][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.826][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.826][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.827][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.830][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.831][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.834][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.835][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:30.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:30.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.837][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.838][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.841][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.842][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.845][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.846][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:30.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:30.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.848][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.849][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.852][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.853][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.856][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.856][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:30.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:30.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.859][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.865][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [62447, 0, 62447, C30H50, InChI=1S/C30H50/c1-21(2)11-9-12-22(3)23-15-19-29(7)24(23)13-14-26-28(6)18-10-17-27(4,5)25(28)16-20-30(26,29)8/h11,23-26H,3,9-10,12-20H2,1-2,4-8H3/t23-,24-,25+,26-,28+,29-,30-/m1/s1, ...]. biodb.DEBUG[2024-07-06 16:04:30.866][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:30.867][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:30.869][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:30.870][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:30.871][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:30.875][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:30.876][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:30.877][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:30.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:30.880][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=480.29*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:30.883][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:30.884][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7269bbea581f1e243800f8ee4e0f4fdb". biodb.TRACE[2024-07-06 16:04:30.885][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:30.886][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7269bbea581f1e243800f8ee4e0f4fdb.content". biodb.DEBUG[2024-07-06 16:04:30.889][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:30.889][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:30.890][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:30.894][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:30.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:30.896][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:30.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:30.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.901][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.905][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.908][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:30.909][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:30.909][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:30.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:30.914][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:30.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:30.916][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:30.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:30.918][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.920][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.921][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.924][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.928][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:30.929][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:30.929][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:30.930][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:30.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:30.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:30.936][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:30.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:30.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.940][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.944][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.945][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:30.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.947][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:30.948][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:30.950][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:30.951][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:30.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:30.956][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:30.956][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:30.957][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:30.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:30.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.962][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.963][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:30.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:30.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.966][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.970][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:30.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:30.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.973][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.974][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:30.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.981][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.984][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:30.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:30.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.988][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.991][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.991][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:30.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:30.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:30.995][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:30.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:30.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:30.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.004][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.007][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.008][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.011][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.012][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.015][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.016][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.018][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.019][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.022][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.023][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.025][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.029][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.030][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.032][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.033][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.036][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.037][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.040][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.040][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.043][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.044][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.047][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.047][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.050][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.051][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.054][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.054][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.057][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.058][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:31.059][private$selectFields] biodb.TRACE[2024-07-06 16:04:31.060][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:31.061][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:31.061][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:31.062][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.063][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.064][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.065][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.066][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.067][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.068][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.068][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.069][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.070][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.071][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.072][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.073][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.074][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.074][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.075][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.076][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.077][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.078][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.079][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.080][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.081][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.081][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.082][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.083][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.084][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.085][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.086][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.087][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.087][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.088][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.089][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.090][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.091][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.092][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.093][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.093][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.094][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.095][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.096][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.097][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.098][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.099][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.100][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.100][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.101][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.102][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.103][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.104][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.105][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.106][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.107][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.107][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.108][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.109][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.110][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.111][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.112][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.113][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.114][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.115][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.116][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.116][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.117][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.118][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.119][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.120][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.121][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.122][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.123][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.123][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.124][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.125][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.126][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.127][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.128][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.129][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.130][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.131][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.131][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.132][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.133][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.134][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.135][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.136][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.137][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.138][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.138][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.139][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.140][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.141][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.142][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.143][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.144][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.145][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.145][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.146][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.147][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.148][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.149][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.150][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.151][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.152][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.152][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.153][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:31.154][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:31.155][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.156][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.157][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.158][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.159][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.160][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.160][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.161][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.162][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.163][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.164][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.165][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.166][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.167][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.167][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.168][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.169][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.170][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.171][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.172][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.173][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.174][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.175][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.175][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.176][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.177][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.178][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.179][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.180][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.181][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.182][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.182][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.183][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.184][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.185][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.186][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.187][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.188][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.189][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.190][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.190][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.191][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.192][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.193][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.194][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.195][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.196][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.197][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.198][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:31.199][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.201][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.208][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.209][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.213][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.217][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.224][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.227][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.231][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.235][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.238][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.246][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.249][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.253][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.256][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.260][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.263][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.264][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.267][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.270][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.271][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.274][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.280][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.283][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.284][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.287][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.287][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.290][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.291][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.294][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.295][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.297][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.298][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.301][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.302][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.305][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.305][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.309][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.313][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.315][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.316][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.319][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.320][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.322][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.323][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.326][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.327][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.329][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.330][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.333][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.339][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [4781, 0, 4781, C29H40N2O4, InChI=1S/C29H40N2O4/c1-6-18-17-31-10-8-20-14-27(33-3)29(35-5)16-23(20)25(31)12-21(18)11-24-22-15-28(34-4)26(32-2)13-19(22)7-9-30-24/h13-16,18,21,24-25,30H,6-12,17H2,1-5H3/t18-,21-,24+,25-/m0/s1, ...]. biodb.DEBUG[2024-07-06 16:04:31.340][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:31.341][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:31.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:31.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:31.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:31.347][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:31.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:31.349][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.351][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.352][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.355][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.356][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.358][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.359][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.362][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.365][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.366][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.369][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.370][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.372][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.373][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.376][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.377][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.380][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.380][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.383][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.384][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.387][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.388][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.390][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.391][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.394][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.395][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.397][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.398][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.401][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.402][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.405][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.405][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.408][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.409][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.412][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.413][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.415][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.416][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.419][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.420][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.422][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.423][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.424][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.426][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.427][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.429][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.430][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.433][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.434][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.437][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.438][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.440][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.441][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:31.442][private$selectFields] biodb.TRACE[2024-07-06 16:04:31.443][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:31.444][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:31.445][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:31.445][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.446][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.447][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.448][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.449][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.450][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.451][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.452][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.453][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.453][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.454][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.455][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.456][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.457][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.458][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.459][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.460][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.461][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.461][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.462][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.463][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.464][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.465][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.466][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.467][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.468][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.468][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.469][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.470][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.471][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.472][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.473][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.474][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.475][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.475][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.476][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.477][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.478][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.479][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.480][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.481][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.482][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.482][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.483][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.484][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.485][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.486][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.487][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.488][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.489][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.490][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.490][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.491][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.492][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.493][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.494][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.495][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.496][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.497][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.497][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.498][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.499][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.500][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.501][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.502][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.503][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.504][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.504][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.505][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.506][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.507][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.508][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.509][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.510][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.511][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.511][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.512][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.513][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.514][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.515][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.516][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.517][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.518][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.518][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.519][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.520][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.521][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.522][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.523][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.524][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.525][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.525][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.526][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.527][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.528][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.529][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.530][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.531][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.532][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.533][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.533][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.534][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.535][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.536][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.537][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:31.538][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:31.539][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.540][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.541][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.541][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.542][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.543][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.544][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.545][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.546][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.547][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.548][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.554][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.555][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.556][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.557][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.558][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.559][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.560][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.560][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.561][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.562][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.563][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.564][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.565][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.566][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.567][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.568][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.568][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.569][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.570][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.571][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.572][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.573][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.574][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.575][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.575][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.576][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.577][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.578][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.579][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.580][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.581][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.581][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.582][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.583][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:31.584][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.587][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.588][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.590][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.593][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.594][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.595][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.598][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.598][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.601][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.602][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.605][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.606][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.608][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.609][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.612][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.613][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.615][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.616][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.619][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.620][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.622][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.623][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.626][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.627][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.630][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.630][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.633][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.634][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.636][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.637][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.640][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.641][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.644][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.645][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.647][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.651][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.652][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.654][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.655][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.659][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.662][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.665][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.669][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.670][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.673][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.673][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.676][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.677][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.680][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.681][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.683][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.687][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.690][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.691][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.694][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.695][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.698][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.699][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.701][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.707][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [91601, 0, 91601, C29H40N2O4, InChI=1S/C29H40N2O4/c1-6-18-17-31-10-8-20-14-27(33-3)29(35-5)16-23(20)25(31)12-21(18)11-24-22-15-28(34-4)26(32-2)13-19(22)7-9-30-24/h13-16,18,21,24-25,30H,6-12,17H2,1-5H3/t18-,21-,24?,25?/m0/s1, ...]. biodb.DEBUG[2024-07-06 16:04:31.708][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:31.709][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:31.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:31.713][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:31.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:31.715][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:31.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:31.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.720][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.722][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.723][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.724][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.727][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.728][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.730][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.734][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.735][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.737][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.738][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.741][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.742][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.744][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.745][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.748][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.749][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.752][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.752][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.755][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.756][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.759][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.760][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.762][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.763][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.766][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.769][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.773][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.774][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.776][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.777][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.780][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.781][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.784][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.784][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.787][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.791][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.794][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.795][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.798][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.799][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.801][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.802][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.805][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.806][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.808][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.809][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:31.810][private$selectFields] biodb.TRACE[2024-07-06 16:04:31.811][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:31.812][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:31.813][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:31.814][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.815][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.815][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.816][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.817][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.818][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.819][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.820][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.821][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.822][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.822][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.829][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.830][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.831][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.832][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.833][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.834][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.835][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.835][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.836][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.837][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.838][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.839][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.840][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.841][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.842][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.843][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.843][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.844][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.845][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.846][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.847][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.848][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.849][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.849][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.850][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.851][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.852][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.853][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.854][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.855][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.855][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.856][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.857][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.858][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.859][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.860][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.861][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.861][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.862][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.863][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.864][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.865][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.866][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.867][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.868][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.868][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.869][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.870][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.871][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.872][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.873][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.874][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.874][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.875][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.876][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.877][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.878][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.879][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.880][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.881][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.881][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.882][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.883][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.884][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.885][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.886][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.887][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:31.887][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.888][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.889][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.890][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.891][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.892][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.893][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.894][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.894][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.895][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.896][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.897][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.898][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.899][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.900][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.901][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.901][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.902][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.903][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.904][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.905][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.906][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.907][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.907][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:31.908][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.909][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.910][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:31.911][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:31.912][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.913][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.914][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.914][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.915][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.916][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.917][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.918][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.919][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.920][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.921][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.921][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.922][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.923][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.924][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.925][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.926][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.927][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.928][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.928][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.929][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:31.930][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:31.931][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.932][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.933][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.934][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:31.935][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.936][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.936][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.937][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:31.938][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.939][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.940][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:31.941][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:31.942][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.943][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.943][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:31.944][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:31.945][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.946][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.947][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:31.948][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:31.949][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.950][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.951][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:31.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.954][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.955][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.958][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:31.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:31.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.961][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.962][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.965][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.966][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.969][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.970][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:31.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:31.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.972][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.973][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.976][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.977][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.980][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.981][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:31.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.983][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.984][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.987][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.988][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.990][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.991][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:31.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:31.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.994][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.995][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:31.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:31.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:31.998][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:31.999][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.001][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.002][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.005][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.006][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.010][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.012][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.013][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.017][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.019][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.020][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.024][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.030][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.034][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.035][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.037][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.038][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.041][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.042][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.045][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.045][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.048][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.049][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.052][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.053][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.055][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.056][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.059][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.060][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.063][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.063][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.066][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.067][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.070][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.075][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [95147, 0, 95147, C29H40N2O4, InChI=1S/C29H40N2O4/c1-3-18-16(2)14-22-20(18)10-11-21-19-6-4-8-26(33)30-13-5-7-24-28(34)27(29(35)31-24)25(32)12-9-17(19)15-23(21)22/h4,8,10-11,16-24,27H,3,5-7,9,12-15H2,1-2H3,(H,30,33)(H,31,35)/t16-,17-,18-,19+,20+,21-,22+,23+,24+,27?/m1/s1, ...]. biodb.DEBUG[2024-07-06 16:04:32.076][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:32.077][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.DEBUG[2024-07-06 16:04:32.080][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:32.081][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:32.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:32.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:32.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:32.087][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:32.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.DEBUG[2024-07-06 16:04:32.090][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.17*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL". biodb.DEBUG[2024-07-06 16:04:32.093][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache. biodb.TRACE[2024-07-06 16:04:32.094][cch$loadFileContent] Trying to load 1 files from cache: [1]: "acfa4b558978abf12409c2b56e678d03". biodb.TRACE[2024-07-06 16:04:32.096][cch$loadFileContent] file.exist = [1]: "TRUE". biodb.TRACE[2024-07-06 16:04:32.097][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/acfa4b558978abf12409c2b56e678d03.content". biodb.DEBUG[2024-07-06 16:04:32.105][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:32.106][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:32.107][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:32.111][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:32.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:32.113][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:32.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:32.114][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.117][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.118][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.121][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.124][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:32.125][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:32.126][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:32.127][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:32.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:32.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:32.132][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:32.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:32.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.137][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.137][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.140][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.144][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:32.145][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:32.145][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:32.146][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:32.150][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:32.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:32.152][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:32.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:32.153][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.156][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.157][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.160][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.161][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.163][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.DEBUG[2024-07-06 16:04:32.164][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame. biodb.DEBUG[2024-07-06 16:04:32.166][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:32.166][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:32.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:32.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:32.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:32.173][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:32.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:32.174][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.177][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.178][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.181][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.181][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.184][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.185][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.188][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.188][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.191][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.192][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.195][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.195][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.198][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.199][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.202][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.203][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.205][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.206][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.209][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.210][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.212][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.213][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.216][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.217][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.219][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.220][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.223][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.224][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.227][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.228][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.228][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.230][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.231][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.234][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.237][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.238][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.241][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.242][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.245][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.245][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.248][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.249][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.252][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.253][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.255][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.256][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.259][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.260][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:32.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:32.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.262][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.263][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:32.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:32.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.266][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.267][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:32.268][private$selectFields] biodb.TRACE[2024-07-06 16:04:32.269][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:32.269][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:32.270][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:32.271][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.272][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.273][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.274][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.275][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.276][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.277][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.277][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.278][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.279][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.280][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.281][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.282][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.283][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.284][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.285][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.285][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.286][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.287][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.288][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.289][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.290][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.291][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.292][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.293][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.293][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.294][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.295][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.296][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.297][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.298][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.299][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.300][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.301][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.301][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.302][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.303][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.304][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.305][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.306][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.307][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.308][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.308][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.309][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.310][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.311][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.312][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.313][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.314][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:32.315][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:32.315][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.316][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.317][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.318][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.319][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.320][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.321][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.322][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.322][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.323][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.324][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.325][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.326][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.327][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.328][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.329][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.330][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.330][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.331][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.332][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.333][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.334][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.335][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.336][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.337][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.337][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.338][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.339][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.340][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.341][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.342][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.343][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.344][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.344][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.345][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.346][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.347][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.348][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.349][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.350][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.351][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.352][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.352][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.353][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.354][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.355][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.356][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.357][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.358][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.359][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.359][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:32.360][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:32.361][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.362][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.363][private$selectFields] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:32.364][private$organizeFieldsByGroups] Fields [12]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:32.365][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.366][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.367][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.368][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.368][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.369][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.370][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.371][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.372][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.373][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.380][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.381][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.382][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.383][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.384][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.385][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.386][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.386][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.387][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.388][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.389][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.390][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.391][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.392][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.393][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.394][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.394][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.395][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.396][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.397][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.398][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.399][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.400][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.401][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.401][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.402][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.403][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.404][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.405][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.406][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.407][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.408][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.408][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.409][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.410][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.411][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.412][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.413][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.414][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "kegg.compound.id", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:32.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.417][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.418][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.421][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.422][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.424][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.425][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.428][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.429][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.432][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.432][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.435][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.438][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.439][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.440][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.442][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.443][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.446][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.447][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.449][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.450][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.453][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.454][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.456][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.457][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.460][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.461][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.464][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.465][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.467][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.468][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.471][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.472][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.474][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.475][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.478][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.479][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.482][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.483][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.485][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.486][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.489][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.490][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.493][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.494][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.496][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.497][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.500][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.501][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.504][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.505][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.505][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.507][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.508][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.511][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.512][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.513][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.514][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.515][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.518][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.519][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.522][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.523][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.525][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.526][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.529][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.530][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.533][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.534][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.536][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.537][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.540][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.541][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.544][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.550][private$entriesToListOfDataframes] Entry converted to data frame: [1, 12]: [accession, charge, chebi.id, formula, inchi, ...] [636, 0, 636, C24H26O6, InChI=1S/C24H26O6/c1-12(2)6-7-14-19-17(11-16(26)22(14)28-5)29-18-10-15(25)13-8-9-24(3,4)30-23(13)20(18)21(19)27/h6,10-11,25-26H,7-9H2,1-5H3, ...]. biodb.DEBUG[2024-07-06 16:04:32.551][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:32.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:32.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:32.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:32.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:32.558][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:32.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:32.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.563][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.564][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.566][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.567][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.570][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.571][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.573][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.574][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.576][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.577][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.581][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.581][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.584][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.585][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.588][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.589][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.591][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.592][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.595][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.596][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.599][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.599][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.601][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.602][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.603][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.606][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.607][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.609][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.610][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.613][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.614][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.616][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.617][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.620][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.624][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.624][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.627][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.628][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.631][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.632][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.634][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.638][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.639][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.641][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.642][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.645][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.646][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:32.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:32.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.649][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.649][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:32.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:32.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.658][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.659][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:32.660][private$selectFields] biodb.TRACE[2024-07-06 16:04:32.661][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:32.662][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:32.663][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:32.664][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.665][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.666][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.666][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.667][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.668][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.669][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.670][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.671][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.672][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.673][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.673][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.674][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.675][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.676][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.677][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.678][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.679][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.680][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.680][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.681][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.682][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.683][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.684][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.685][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.686][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.687][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.687][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.688][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.689][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.690][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.691][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.692][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.693][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.694][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.694][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.695][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.696][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.697][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.698][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.699][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.700][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.701][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.701][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.702][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.703][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.704][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.705][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.706][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:32.707][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:32.708][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.708][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.709][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.710][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.711][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.712][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.713][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.714][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.715][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.715][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.716][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.717][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.718][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.719][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.720][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.721][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.721][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.722][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.723][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.724][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.725][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.726][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.727][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.728][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.728][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.729][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.730][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.731][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.732][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.733][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.734][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.735][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.735][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.736][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.737][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.738][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.739][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.740][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.741][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.742][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.742][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.743][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.744][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.745][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.746][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.747][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.748][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.748][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.749][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.750][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.751][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:32.752][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:32.753][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.754][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.755][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:32.756][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:32.756][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.757][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.758][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.759][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.760][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.761][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.762][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.763][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.764][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.765][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.765][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.766][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.767][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.768][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.769][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.770][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.771][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.772][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.772][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.773][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.774][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.775][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.776][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.777][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.778][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.779][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.780][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.780][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.781][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.782][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.783][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.784][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.785][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.786][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.787][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.788][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.788][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.789][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.790][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.791][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.792][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.793][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.794][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.795][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.796][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:32.797][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.799][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.800][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.803][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.806][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.807][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.810][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.811][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.813][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.814][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.815][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.817][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.818][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.821][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.822][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.825][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.826][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.828][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.829][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.832][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.833][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.836][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.837][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.839][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.840][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.841][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.842][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.843][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.844][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.846][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.847][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.850][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.851][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.854][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.855][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.857][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.858][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.861][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.862][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.864][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.865][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.868][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.869][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.872][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.873][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.875][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.876][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.879][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.880][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.882][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.883][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.886][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.887][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.890][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.890][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:32.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:32.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.893][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.894][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.897][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.898][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.900][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.901][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:32.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:32.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.904][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.905][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.908][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.908][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.911][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.912][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:32.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:32.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.915][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.920][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [64199, 0, 64199, C24H27ClN2O2, InChI=1S/C24H26N2O2.ClH/c27-24(28)20-9-10-23-22(16-20)21(17-25-23)8-4-5-13-26-14-11-19(12-15-26)18-6-2-1-3-7-18;/h1-3,6-7,9-11,16-17,25H,4-5,8,12-15H2,(H,27,28);1H, ...]. biodb.DEBUG[2024-07-06 16:04:32.921][notifyObservers] Notify observers for notifyProgress. biodb.DEBUG[2024-07-06 16:04:32.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:32.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:32.933][FUN] Trying to call function notifyProgress on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:32.934][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:32.935][FUN] Trying to call function notifyProgress on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:32.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". biodb.TRACE[2024-07-06 16:04:32.936][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.939][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:32.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:32.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.943][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.944][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.946][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.947][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:32.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:32.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.950][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.951][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.953][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.954][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:32.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.957][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.958][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.960][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.961][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:32.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:32.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.964][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.965][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.967][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.968][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:32.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:32.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.971][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.972][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.974][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.975][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:32.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:32.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.978][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.979][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.981][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.982][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:32.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.985][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.986][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.988][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.989][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:32.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.992][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.993][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.995][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:32.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:32.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:32.999][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.000][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:33.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:33.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.002][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.003][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:33.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:33.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.006][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.007][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:33.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:33.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.009][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.010][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:33.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:33.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.013][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.014][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:33.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:33.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.016][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.017][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:33.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:33.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.020][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.021][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:33.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:33.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.023][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.024][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:33.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:33.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.027][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.028][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:33.029][private$selectFields] biodb.TRACE[2024-07-06 16:04:33.030][private$selectFields] Fields is null: FALSE biodb.TRACE[2024-07-06 16:04:33.030][private$selectFields] Fields.type is null: TRUE biodb.TRACE[2024-07-06 16:04:33.031][private$selectFields] Fields [13]: "accession, charge, chebi.id, formula, inchi, inchikey, kegg.compound.id, molecular.mass, monoisotopic.mass, n.stars, ..." biodb.TRACE[2024-07-06 16:04:33.032][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:33.033][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:33.034][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.035][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.036][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:33.037][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:33.038][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.038][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.039][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:33.040][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:33.041][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.042][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.043][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:33.044][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:33.045][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.045][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.046][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:33.047][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:33.048][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.049][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.050][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:33.051][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:33.052][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.053][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.053][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:33.054][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:33.055][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.056][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.057][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:33.058][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:33.059][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.060][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.061][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:33.061][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:33.062][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.063][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.064][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:33.065][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:33.066][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.067][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.068][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:33.069][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:33.069][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.070][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.071][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:33.072][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:33.073][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.074][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.075][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:33.076][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:33.077][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.078][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.078][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:33.079][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:33.080][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.081][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.082][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:33.083][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:33.084][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.085][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.086][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:33.087][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:33.088][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.088][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.089][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:33.090][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:33.091][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.092][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.093][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:33.094][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:33.095][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.095][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.096][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:33.097][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:33.098][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.099][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.100][ef$get] Asked field names are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:33.101][ef$get] Realnames of fields are: kegg.compound.id. biodb.TRACE[2024-07-06 16:04:33.102][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.102][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.103][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:33.104][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:33.105][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.106][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.107][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:33.108][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:33.109][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.109][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.110][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:33.111][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:33.112][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.113][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.114][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:33.115][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:33.116][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.116][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.117][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:33.118][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:33.119][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.120][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.121][ef$get] Asked field names are: peak.attr. biodb.TRACE[2024-07-06 16:04:33.122][ef$get] Realnames of fields are: peak.attr. biodb.TRACE[2024-07-06 16:04:33.123][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.124][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.124][private$selectFields] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:33.125][private$organizeFieldsByGroups] Fields [11]: "accession, charge, chebi.id, formula, inchi, inchikey, molecular.mass, monoisotopic.mass, n.stars, name, ..." biodb.TRACE[2024-07-06 16:04:33.126][ef$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:33.127][ef$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:33.128][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.129][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.130][ef$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:33.131][ef$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:33.132][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.132][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.133][ef$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:33.134][ef$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:33.135][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.136][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.137][ef$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:33.138][ef$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:33.139][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.139][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.140][ef$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:33.141][ef$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:33.142][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.143][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.144][ef$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:33.145][ef$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:33.146][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.146][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.147][ef$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:33.148][ef$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:33.149][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.150][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.151][ef$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:33.152][ef$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:33.153][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.153][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.154][ef$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:33.155][ef$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:33.156][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.157][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.158][ef$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:33.159][ef$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:33.160][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.160][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.161][ef$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:33.162][ef$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:33.163][ef$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.164][ef$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.165][private$organizeFieldsByGroups] Groups [2]: "c("accession", "charge", "chebi.id", "formula", "inchi", "inchikey", "molecular.mass", "monoisotopic.mass", "n.stars", "name", "smiles"), list()" biodb.TRACE[2024-07-06 16:04:33.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:33.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:33.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.168][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:33.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:33.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.172][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.173][self$getBiodb()$getEntryFields()$get] Asked field names are: accession. biodb.TRACE[2024-07-06 16:04:33.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession. biodb.TRACE[2024-07-06 16:04:33.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.175][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.176][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:33.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:33.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.179][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.180][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:33.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:33.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.183][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.184][self$getBiodb()$getEntryFields()$get] Asked field names are: charge. biodb.TRACE[2024-07-06 16:04:33.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge. biodb.TRACE[2024-07-06 16:04:33.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.186][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:33.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:33.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.190][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.191][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:33.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:33.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.194][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.194][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id. biodb.TRACE[2024-07-06 16:04:33.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id. biodb.TRACE[2024-07-06 16:04:33.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.197][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.198][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:33.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:33.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.207][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.208][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:33.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:33.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.210][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.211][self$getBiodb()$getEntryFields()$get] Asked field names are: formula. biodb.TRACE[2024-07-06 16:04:33.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula. biodb.TRACE[2024-07-06 16:04:33.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.214][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.215][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:33.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:33.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.218][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.219][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:33.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:33.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.221][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.222][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi. biodb.TRACE[2024-07-06 16:04:33.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi. biodb.TRACE[2024-07-06 16:04:33.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.225][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.226][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:33.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:33.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.228][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.229][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:33.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:33.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.232][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.233][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey. biodb.TRACE[2024-07-06 16:04:33.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey. biodb.TRACE[2024-07-06 16:04:33.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.235][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.236][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:33.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:33.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.239][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.240][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:33.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:33.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.242][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.243][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass. biodb.TRACE[2024-07-06 16:04:33.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass. biodb.TRACE[2024-07-06 16:04:33.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.246][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.247][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:33.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:33.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.250][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:33.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:33.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.253][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.254][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:33.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass. biodb.TRACE[2024-07-06 16:04:33.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.257][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.258][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:33.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:33.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.260][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.261][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:33.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:33.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.264][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.265][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars. biodb.TRACE[2024-07-06 16:04:33.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars. biodb.TRACE[2024-07-06 16:04:33.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.267][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.268][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:33.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:33.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.271][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.272][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:33.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:33.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.275][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name. biodb.TRACE[2024-07-06 16:04:33.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name. biodb.TRACE[2024-07-06 16:04:33.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.278][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.279][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:33.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:33.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.282][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.283][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:33.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:33.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.285][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.286][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles. biodb.TRACE[2024-07-06 16:04:33.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles. biodb.TRACE[2024-07-06 16:04:33.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.289][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.295][private$entriesToListOfDataframes] Entry converted to data frame: [1, 11]: [accession, charge, chebi.id, formula, inchi, ...] [65648, 0, 65648, C24H26O6, InChI=1S/C24H26O6/c1-13(2)9-10-23-20(27)22(28-5)11-14-19(26)18-15(25)7-6-8-16(18)29-24(14,23)17(12-22)21(3,4)30-23/h6-9,11,17,25H,10,12H2,1-5H3/t17-,22-,23-,24+/m0/s1, ...]. biodb.DEBUG[2024-07-06 16:04:33.295][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s). biodb.DEBUG[2024-07-06 16:04:33.296][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries. biodb.TRACE[2024-07-06 16:04:33.302][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-07-06 16:04:33.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-07-06 16:04:33.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.304][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.305][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-07-06 16:04:33.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-07-06 16:04:33.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.308][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.TRACE[2024-07-06 16:04:33.309][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass. biodb.TRACE[2024-07-06 16:04:33.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass. biodb.TRACE[2024-07-06 16:04:33.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned. biodb.TRACE[2024-07-06 16:04:33.312][self$getBiodb()$getEntryFields()$get] fields variable is a list. biodb.INFO [2024-07-06 16:04:33.315][biodb$terminate] Closing BiodbMain instance... biodb.DEBUG[2024-07-06 16:04:33.316][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler biodb.INFO [2024-07-06 16:04:33.317][self$deleteConn] Connector "chebi" deleted. biodb.DEBUG[2024-07-06 16:04:33.318][notifyObservers] Notify observers for terminate. biodb.DEBUG[2024-07-06 16:04:33.318][FUN] Trying to call function terminate on observer BiodbTestMsgAck. biodb.DEBUG[2024-07-06 16:04:33.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize". biodb.DEBUG[2024-07-06 16:04:33.320][FUN] Trying to call function terminate on observer BiodbEntryFields. biodb.DEBUG[2024-07-06 16:04:33.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize". biodb.DEBUG[2024-07-06 16:04:33.322][FUN] Trying to call function terminate on observer BiodbConfig. biodb.DEBUG[2024-07-06 16:04:33.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize". [ FAIL 0 | WARN 0 | SKIP 0 | PASS 1372 ] > > proc.time() user system elapsed 83.358 1.599 176.018
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --test-dir=longtests --no-stop-on-test-error --no-codoc --no-examples --no-manual --ignore-vignettes --check-subdirs=no biodbChebi_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc-longtests/meat/biodbChebi.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * using options ‘--no-codoc --no-examples --no-manual --ignore-vignettes --no-stop-on-test-error’ * checking for file ‘biodbChebi/DESCRIPTION’ ... OK * this is package ‘biodbChebi’ version ‘1.11.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘biodbChebi’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... SKIPPED * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... SKIPPED * checking examples ... SKIPPED * checking for unstated dependencies in ‘longtests’ ... OK * checking tests in ‘longtests’ ... Running ‘testthat.R’ OK * DONE Status: OK
biodbChebi.Rcheck/00install.out
* installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)